Publications by authors named "Seema R Lalani"

105 Publications

A rare description of pure partial trisomy of 16q12.2q24.3 and review of the literature.

Am J Med Genet A 2021 10 1;185(10):2903-2912. Epub 2021 Jun 1.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

Trisomy 16 is the most common autosomal trisomy in humans, which is almost uniformly embryonic lethal. Partial trisomy 16 including a segment of the long arm of chromosome 16 is occasionally compatible with life and has been associated with severe congenital defects, growth retardation, and early lethality. Segmental trisomy of 16q is usually described concomitantly with partial monosomy of another chromosome, often resulting from a parental balanced translocation. Pure partial chromosome 16q trisomy is exceedingly rare. About nine children with 16q12→qter and 16q13→qter duplication have been reported in the literature, almost all described with monosomy of a second chromosome, and highlighting very few long-term survivors. A single individual with pure partial distal 16q12.1q23.3 duplication has been reported in an infant, underscoring complexities of genetic counseling and management, especially in view of life-limiting congenital anomalies in rare survivors. Here, we present a 12-month-old child with pure 16q12.2q24.3 trisomy, having continued morbidity related to pulmonary hypertension and chronic lung disease. The features of intrauterine growth retardation, facial dysmorphism, hypotonia, congenital heart defect, distal contractures, urogenital abnormalities, and hearing loss support the association with 16q partial trisomy, as in previous studies. This report expands our current understanding related to the survival of infants with large segmental aneusomy of the long arm of chromosome 16.
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http://dx.doi.org/10.1002/ajmg.a.62368DOI Listing
October 2021

PPP3CA truncating variants clustered in the regulatory domain cause early-onset refractory epilepsy.

Clin Genet 2021 08 1;100(2):227-233. Epub 2021 Jun 1.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

PPP3CA encodes the catalytic subunit of calcineurin, a calcium-calmodulin-regulated serine-threonine phosphatase. Loss-of-function (LoF) variants in the catalytic domain have been associated with epilepsy, while gain-of-function (GoF) variants in the auto-inhibitory domain cause multiple congenital abnormalities. We herein report five new patients with de novo PPP3CA variants. Interestingly, the two frameshift variants in this study and the six truncating variants reported previously are all located within a 26-amino acid region in the regulatory domain (RD). Patients with a truncating variant had more severe earlier onset seizures compared to patients with a LoF missense variant, while autism spectrum disorder was a more frequent feature in the latter. Expression studies of a truncating variant showed apparent RNA expression from the mutant allele, but no detectable mutant protein. Our data suggest that PPP3CA truncating variants clustered in the RD, causing more severe early-onset refractory epilepsy and representing a type of variants distinct from LoF or GoF missense variants.
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http://dx.doi.org/10.1111/cge.13979DOI Listing
August 2021

Haploinsufficiency of PRR12 causes a spectrum of neurodevelopmental, eye, and multisystem abnormalities.

Genet Med 2021 07 6;23(7):1234-1245. Epub 2021 Apr 6.

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.

Purpose: Proline Rich 12 (PRR12) is a gene of unknown function with suspected DNA-binding activity, expressed in developing mice and human brains. Predicted loss-of-function variants in this gene are extremely rare, indicating high intolerance of haploinsufficiency.

Methods: Three individuals with intellectual disability and iris anomalies and truncating de novo PRR12 variants were described previously. We add 21 individuals with similar PRR12 variants identified via matchmaking platforms, bringing the total number to 24.

Results: We observed 12 frameshift, 6 nonsense, 1 splice-site, and 2 missense variants and one patient with a gross deletion involving PRR12. Three individuals had additional genetic findings, possibly confounding the phenotype. All patients had developmental impairment. Variable structural eye defects were observed in 12/24 individuals (50%) including anophthalmia, microphthalmia, colobomas, optic nerve and iris abnormalities. Additional common features included hypotonia (61%), heart defects (52%), growth failure (54%), and kidney anomalies (35%). PrediXcan analysis showed that phecodes most strongly associated with reduced predicted PRR12 expression were enriched for eye- (7/30) and kidney- (4/30) phenotypes, such as wet macular degeneration and chronic kidney disease.

Conclusion: These findings support PRR12 haploinsufficiency as a cause for a novel disorder with a wide clinical spectrum marked chiefly by neurodevelopmental and eye abnormalities.
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http://dx.doi.org/10.1038/s41436-021-01129-6DOI Listing
July 2021

Variants Associated With X-Linked Intellectual Disability and Congenital Malformation.

Front Cell Dev Biol 2021 3;9:631428. Epub 2021 Mar 3.

Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.

Background: X-linked intellectual disability (XLID), which occurs predominantly in males, is a relatively common and genetically heterogeneous disorder in which over 100 mutated genes have been reported. The gene at Xp11.23 encodes ovarian tumor deubiquitinase 5 protein, which is a deubiquitinating enzyme member of the ovarian tumor family. LINKage-specific-deubiquitylation-deficiency-induced embryonic defects (LINKED) syndrome, arising from pathogenic variants, was recently reported as a new XLID with additional congenital anomalies.

Methods: We investigated three affected males (49- and 47-year-old brothers [Individuals 1 and 2] and a 2-year-old boy [Individual 3]) from two families who showed developmental delay. Their common clinical features included developmental delay, hypotonia, short stature, and distinctive facial features, such as telecanthus and a depressed nasal bridge. Individuals 1 and 2 showed epilepsy and brain magnetic resonance imaging showed a thin corpus callosum and mild ventriculomegaly. Individual 3 showed congenital malformations, including tetralogy of Fallot, hypospadias, and bilateral cryptorchidism. To identify the genetic cause of these features, we performed whole-exome sequencing.

Results: A hemizygous missense variant, c.878A>T, p.Asn293Ile [NM_017602.4], was identified in one family with Individuals 1 and 2, and another missense variant, c.1210 C>T, p.Arg404Trp, in the other family with Individual 3, respectively. The former variant has not been registered in public databases and was predicted to be pathogenic by multiple prediction tools. The latter variant p.Arg404Trp was previously reported as a pathogenic variant, and Individual 3 showed a typical LINKED syndrome phenotype. However, Individuals 1 and 2, with the novel variant (p.Asn293Ile), showed no cardiac or genitourinary malformations.

Conclusions: Unlike previous reports of LINKED syndrome, which described early lethality with congenital cardiac anomalies, our three cases are still alive. Notably, the adult brothers with the novel missense variant have lived into their forties. This may be indicative of a milder phenotype as a possible genotype-phenotype correlation. These findings imply a possible long-term prognosis for individuals with this new XLID syndrome, and a wider phenotypic variation than initially thought.
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http://dx.doi.org/10.3389/fcell.2021.631428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7965969PMC
March 2021

Clinical exome sequencing data reveal high diagnostic yields for congenital diaphragmatic hernia plus (CDH+) and new phenotypic expansions involving CDH.

J Med Genet 2021 Jan 18. Epub 2021 Jan 18.

Texas Children's Hospital, Houston, Texas, USA

Background: Congenital diaphragmatic hernia (CDH) is a life-threatening birth defect that often co-occurs with non-hernia-related anomalies (CDH+). While copy number variant (CNV) analysis is often employed as a diagnostic test for CDH+, clinical exome sequencing (ES) has not been universally adopted.

Methods: We analysed a clinical database of ~12 000 test results to determine the diagnostic yields of ES in CDH+ and to identify new phenotypic expansions.

Results: Among the 76 cases with an indication of CDH+, a molecular diagnosis was made in 28 cases for a diagnostic yield of 37% (28/76). A provisional diagnosis was made in seven other cases (9%; 7/76). Four individuals had a diagnosis of Kabuki syndrome caused by frameshift variants in . Putatively deleterious variants in and were each found in two individuals, supporting their role in CDH development. We also identified individuals with de novo pathogenic variants in and , and compound heterozygous pathogenic variants in . The role of these genes in CDH development is supported by the expression of their mouse homologs in the developing diaphragm, their high CDH-specific pathogenicity scores generated using a previously validated algorithm for genome-scale knowledge synthesis and previously published case reports.

Conclusion: We conclude that ES should be ordered in cases of CDH+ when a specific diagnosis is not suspected and CNV analyses are negative. Our results also provide evidence in favour of phenotypic expansions involving CDH for genes associated with -congenital disorder of glycosylation, Rubinstein-Taybi syndrome, Fanconi anaemia, Coffin-Siris syndrome and -related disorders.
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http://dx.doi.org/10.1136/jmedgenet-2020-107317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8286264PMC
January 2021

Corrigendum: Overgrowth Syndromes-Evaluation, Diagnosis, and Management.

Front Pediatr 2020 23;8:624141. Epub 2020 Dec 23.

Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States.

[This corrects the article DOI: 10.3389/fped.2020.574857.].
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http://dx.doi.org/10.3389/fped.2020.624141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787193PMC
December 2020

Vertical transmission of a large calvarial ossification defect due to heterozygous variants of ALX4 and TWIST1.

Am J Med Genet A 2021 03 27;185(3):916-922. Epub 2020 Dec 27.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

ALX4 is a homeobox gene expressed in the mesenchyme of developing bone and is known to play an important role in the regulation of osteogenesis. Enlarged parietal foramina (EPF) is a phenotype of delayed intramembranous ossification of calvarial bones due to variants of ALX4. The contrasting phenotype of premature ossification of sutures is observed with heterozygous loss-of-function variants of TWIST1, which is an important regulator of osteoblast differentiation. Here, we describe an individual with a large cranium defect, with dominant transmission from the mother, both carrying disease causing heterozygous variants in ALX4 and TWIST1. The distinct phenotype of absent superior and posterior calvarium in the child and his mother was in sharp contrast to the other affected maternal relatives with a recognizable ALX4-related EPF phenotype. This report demonstrates comorbid disorders of Saethre-Chotzen syndrome and EPF in a mother and her child, resulting in severe skull defects reminiscent of calvarial abnormalities observed with bilallelic ALX4 variants. To our knowledge this is the first instance of ALX4 and TWIST1 variants acting synergistically to cause a unique phenotype influencing skull ossification.
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http://dx.doi.org/10.1002/ajmg.a.62036DOI Listing
March 2021

Overgrowth Syndromes-Evaluation, Diagnosis, and Management.

Front Pediatr 2020 30;8:574857. Epub 2020 Oct 30.

Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States.

Abnormally excessive growth results from perturbation of a complex interplay of genetic, epigenetic, and hormonal factors that orchestrate human growth. Overgrowth syndromes generally present with inherent health concerns and, in some instances, an increased risk of tumor predisposition that necessitate prompt diagnosis and appropriate referral. In this review, we introduce some of the more common overgrowth syndromes, along with their molecular mechanisms, diagnostics, and medical complications for improved recognition and management of patients affected with these disorders.
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http://dx.doi.org/10.3389/fped.2020.574857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7661798PMC
October 2020

Sudden infant death with dysgenesis of the testes syndrome in a non-Amish infant: A case report.

Am J Med Genet A 2020 11 4;182(11):2751-2754. Epub 2020 Sep 4.

Baylor College of Medicine, Houston, Texas, USA.

Sudden Infant Death with Dysgenesis of the Testes syndrome (SIDDT) is a very rare condition associated with biallelic pathogenic variants in the TSPYL1 gene first reported in 2004. It is characterized by sudden cardiac or respiratory arrest, disordered testicular development, neurologic dysfunction, and is uniformly fatal before the age of 12 months. There were previously 21 reported cases of SIDDT in the literature, all from nine Old Order Amish families published in a single paper. In this report, we describe a non-Amish, phenotypically female infant with poor feeding and abnormal motor movements noted at birth. Initial testing showed that she had a 46,XY chromosome complement, and chromosomal microarray showed a significant absence of heterozygosity (AOH) totalling roughly 600 Mb across multiple different chromosomes, indicating consanguinity. Further workup with exome sequencing revealed homozygosity for a frameshift variant in TSPYL1 (c.725_726delTG, p.Val242GlufsTer52) consistent with a diagnosis of SIDDT, explaining many of her clinical features. However, she was also noted to have a mild T-cell lymphopenia and developed intractable epilepsy after hospital discharge. These features have not previously been reported in SIDDT and may represent phenotypic expansion. To our knowledge, this patient is the 22nd case of SIDDT to be reported in the literature, and the first to be of non-Amish heritage.
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http://dx.doi.org/10.1002/ajmg.a.61842DOI Listing
November 2020

Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing.

Am J Hum Genet 2020 09 29;107(3):544-554. Epub 2020 Jul 29.

University of South Dakota, Sanford School of Medicine, Sioux Falls, SD 57105, USA.

RNA polymerase II interacts with various other complexes and factors to ensure correct initiation, elongation, and termination of mRNA transcription. One of these proteins is SR-related CTD-associated factor 4 (SCAF4), which is important for correct usage of polyA sites for mRNA termination. Using exome sequencing and international matchmaking, we identified nine likely pathogenic germline variants in SCAF4 including two splice-site and seven truncating variants, all residing in the N-terminal two thirds of the protein. Eight of these variants occurred de novo, and one was inherited. Affected individuals demonstrated a variable neurodevelopmental disorder characterized by mild intellectual disability, seizures, behavioral abnormalities, and various skeletal and structural anomalies. Paired-end RNA sequencing on blood lymphocytes of SCAF4-deficient individuals revealed a broad deregulation of more than 9,000 genes and significant differential splicing of more than 2,900 genes, indicating an important role of SCAF4 in mRNA processing. Knockdown of the SCAF4 ortholog CG4266 in the model organism Drosophila melanogaster resulted in impaired locomotor function, learning, and short-term memory. Furthermore, we observed an increased number of active zones in larval neuromuscular junctions, representing large glutamatergic synapses. These observations indicate a role of CG4266 in nervous system development and function and support the implication of SCAF4 in neurodevelopmental phenotypes. In summary, our data show that heterozygous, likely gene-disrupting variants in SCAF4 are causative for a variable neurodevelopmental disorder associated with impaired mRNA processing.
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http://dx.doi.org/10.1016/j.ajhg.2020.06.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477272PMC
September 2020

A novel CACNA1A variant in a child with early stroke and intractable epilepsy.

Mol Genet Genomic Med 2020 10 21;8(10):e1383. Epub 2020 Jul 21.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

Background: CACNA1A variants have been described in several disorders that encompass a wide range of neurologic phenotypes, including hemiplegic migraine, ataxia, cognitive delay, and epilepsy. To date, ischemic stroke caused by a CACNA1A variant has only been reported once in the literature.

Methods: We describe a 4-year-old female with recurrent ischemic strokes beginning at 6 weeks of age, intractable epilepsy, and significant global developmental delay. Exome sequencing (ES) was completed for her evaluation.

Results: We found a novel de novo, likely pathogenic variant, p.Leu1692Gln in CACNA1A by ES. The substitution affects a leucine residue that is highly conserved in species from fish to primates.

Conclusion: We present the second case of recurrent ischemic strokes in a patient with CACNA1A mutation. Our findings expand the phenotypic heterogeneity related to Ca 2.1 (P/Q-type) calcium channel dysfunction and suggest consideration of CACNA1A disorder in evaluation of pediatric strokes.
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http://dx.doi.org/10.1002/mgg3.1383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7549575PMC
October 2020

An Analysis of Hospital Mortality After Cardiac Operations in Children With Down Syndrome.

Semin Thorac Cardiovasc Surg 2020 Winter;32(4):947-957. Epub 2020 Jul 2.

Lillie Frank Abercrombie Section of Cardiology, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas.

Children with Down syndrome (DS) have lower mortality compared to nonsyndromic (NS) children after atrioventricular septal defect (AVSD) repair. Limited data exist regarding hospital mortality and utilization after other congenital heart disease (CHD) operations in DS. We compared hospital mortality and utilization after CHD operations in both populations and hypothesized that the survival benefit in children with DS is not consistent across CHD lesions. The Texas Inpatient Public Use Datafile was queried for all patients <18 years old undergoing operations for CHD between 1999 and 2016. Hospital mortality, length-of-stay and charges were compared between DS and NS groups, stratified by CHD operation using mixed-effects multivariable analyses and propensity score matching analyses adjusting for prematurity, low birth weight, age, and sex. Over the 18-year period, 2841 cases with DS underwent CHD operations compared to 25,063 NS cases. The most common types of interventions performed in DS were AVSD repair, isolated ventricular septal defect (VSD) repair and tetralogy of Fallot (TOF) repair. By multivariable analyses, DS was associated with lower mortality after isolated AVSD repair (RR 0.40 [IQR 0.20-0.79]), and higher hospital mortality after bidirectional Glenn anastomosis (BDG) (RR 5.17 [IQR 2.10-12.77]) and TOF/pulmonary atresia repair (RR 9.71 [IQR 2.16-43.68]) compared to NS children. Similar results were noted using propensity score matching. Children with DS had lower mortality after AVSD repair than NS children, but higher mortality after operations for BDG and TOF/pulmonary atresia. Further study is needed to determine if the presence of pulmonary hypertension in DS modifies the association between DS and mortality depending on cardiac lesion.
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http://dx.doi.org/10.1053/j.semtcvs.2020.06.037DOI Listing
April 2021

Recessive ACO2 variants as a cause of isolated ophthalmologic phenotypes.

Am J Med Genet A 2020 08 25;182(8):1960-1966. Epub 2020 May 25.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

The mitochondrial aconitase gene (ACO2) encodes an enzyme that catalyzes the conversion of citrate to isocitrate in the tricarboxylic acid cycle. Biallelic variants in ACO2 are purported to cause two distinct disorders: infantile cerebellar-retinal degeneration (ICRD) which is characterized by CNS abnormalities, neurodevelopmental phenotypes, optic atrophy and retinal degeneration; and optic atrophy 9 (OPA9), characterized by isolated ophthalmologic phenotypes including optic atrophy and low vision. However, some doubt remains as to whether biallelic ACO2 variants can cause isolated ophthalmologic phenotypes. A review of the literature revealed five individuals from three families who carry biallelic ACO2 variants whose phenotypes are consistent with OPA9. Here, we describe a brother and sister with OPA9 who are compound heterozygous for novel missense variants in ACO2; c.[487G>T];[1894G>A], p.[(Val163Leu)];[(Val632Met)]. A review of pathogenic ACO2 variants revealed that those associated with OPA9 are distinct from those associated with ICRD. Missense variants associated with either OPA9 or ICRD do not cluster in distinct ACO2 domains, making it difficult to predict the severity of a variant based on position alone. We conclude that biallelic variants in ACO2 can cause the milder OPA9 phenotype, and that the OPA9-related ACO2 variants identified to date are distinct from those that cause ICRD.
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http://dx.doi.org/10.1002/ajmg.a.61634DOI Listing
August 2020

Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings.

Genomics 2020 09 6;112(5):2937-2941. Epub 2020 May 6.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

To further assess the scale and level of parental somatic mosaicism, we queried the CMA database at Baylor Genetics. We selected 50 unrelated families where clinically relevant apparent de novo CNV-deletions were found in the affected probands. Parental blood samples screening using deletion junction-specific PCR revealed four parents with somatic mosaicism. Droplet digital PCR (ddPCR), qPCR, and amplicon-based next-generation sequencing (NGS) were applied to validate these findings. Using ddPCR levels of mosaicism ranged from undetectable to 18.5%. Amplicon-based NGS and qPCR for the father with undetectable mosaicism was able to detect mosaicism at 0.39%. In one mother, ddPCR analysis revealed 15.6%, 10.6%, 8.2%, and undetectable levels of mosaicism in her blood, buccal cells, saliva, and urine samples, respectively. Our data suggest that more sensitive and precise methods, e.g. CNV junction-specific LR-PCR, ddPCR, or qPCR may allow for a more refined assessment of the potential disease recurrence risk for an identified variant.
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http://dx.doi.org/10.1016/j.ygeno.2020.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363577PMC
September 2020

Exome sequencing compared with standard genetic tests for critically ill infants with suspected genetic conditions.

Genet Med 2020 08 27;22(8):1303-1310. Epub 2020 Apr 27.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

Purpose: As exome sequencing (ES) is increasingly used as a diagnostic tool, we aimed to compare ES with status quo genetic diagnostic workup for infants with suspected genetic disorders in terms of identifying diagnoses, survival, and cost of care.

Methods: We studied newborns and infants admitted to intensive care with a suspected genetic etiology within the first year of life at a US quaternary-referral children's hospital over 5 years. In this propensity-matched cohort study using electronic medical record data, we compared patients who received ES as part of a diagnostic workup (ES cohort, n = 368) with clinically similar patients who did not receive ES (No-ES cohort, n = 368).

Results: Diagnostic yield (27.4% ES, 25.8% No-ES; p = 0.62) and 1-year survival (80.2% ES, 84.8% No-ES; p = 0.10) were no different between cohorts. ES cohort patients had higher cost of admission, diagnostic investigation, and genetic testing (all p < 0.01).

Conclusion: ES did not differ from status quo genetic testing collectively in terms of diagnostic yield or patient survival; however, it had high yield as a single test, led to complementary classes of diagnoses, and was associated with higher costs. Further work is needed to define the most efficient use of diagnostic ES for critically ill newborns and infants.
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http://dx.doi.org/10.1038/s41436-020-0798-1DOI Listing
August 2020

Wolff-Parkinson-White syndrome: De novo variants and evidence for mutational burden in genes associated with atrial fibrillation.

Am J Med Genet A 2020 06 31;182(6):1387-1399. Epub 2020 Mar 31.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

Background: Wolff-Parkinson-White (WPW) syndrome is a relatively common arrhythmia affecting ~1-3/1,000 individuals. Mutations in PRKAG2 have been described in rare patients in association with cardiomyopathy. However, the genetic basis of WPW in individuals with a structurally normal heart remains poorly understood. Sudden death due to atrial fibrillation (AF) can also occur in these individuals. Several studies have indicated that despite ablation of an accessory pathway, the risk of AF remains high in patients compared to general population.

Methods: We applied exome sequencing in 305 subjects, including 65 trios, 80 singletons, and 6 multiple affected families. We used de novo analysis, candidate gene approach, and burden testing to explore the genetic contributions to WPW.

Results: A heterozygous deleterious variant in PRKAG2 was identified in one subject, accounting for 0.6% (1/151) of the genetic basis of WPW in this study. Another individual with WPW and left ventricular hypertrophy carried a known pathogenic variant in MYH7. We found rare de novo variants in genes associated with arrhythmia and cardiomyopathy (ANK2, NEBL, PITX2, and PRDM16) in this cohort. There was an increased burden of rare deleterious variants (MAF ≤ 0.005) with CADD score ≥ 25 in genes linked to AF in cases compared to controls (P = .0023).

Conclusions: Our findings show an increased burden of rare deleterious variants in genes linked to AF in WPW syndrome, suggesting that genetic factors that determine the development of accessory pathways may be linked to an increased susceptibility of atrial muscle to AF in a subset of patients.
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http://dx.doi.org/10.1002/ajmg.a.61571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275694PMC
June 2020

Other genomic disorders and congenital heart disease.

Authors:
Seema R Lalani

Am J Med Genet C Semin Med Genet 2020 03 7;184(1):107-115. Epub 2020 Jan 7.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.

Congenital heart disease (CHD) is the common birth defect worldwide. Despite its recognized burden on public health, the etiology in the vast majority of individuals remains unknown. Chromosomal abnormality plays an important role, frequently observed as large cytogenetically visible rearrangement or small submicroscopic structural variation in the genome. Several genomic disorders are now recognized that are increasingly responsible for CHD with variable penetrance. Single gene disorders, epigenetic alterations, and environmental etiologies are also significant contributors. Our understanding of the genetic basis of CHD has increased exponentially with the escalating use of next generation sequencing to identify ever so small submicroscopic genomic imbalances at the level of coding exons in CHD. This review focuses on genomic disorders other than 22q11.2 deletion, that are major players in the etiology of human cardiac malformations.
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http://dx.doi.org/10.1002/ajmg.c.31762DOI Listing
March 2020

A de novo variant in the human HIST1H4J gene causes a syndrome analogous to the HIST1H4C-associated neurodevelopmental disorder.

Eur J Hum Genet 2020 05 5;28(5):674-678. Epub 2019 Dec 5.

Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands.

We report here a de novo missense variant in HIST1H4J resulting in a complex syndrome combining growth delay, microcephaly and intellectual disability. Trio whole exome sequencing (WES) revealed that the proband was heterozygous for a de novo c.274 A > G p.(K91E) variant in HIST1H4J, a gene not yet associated with human disease. The patient presented with profound intellectual disability, microcephaly, and dysmorphic facial features. Functional consequences of the identified de novo missense variant were evaluated in zebrafish embryos, where they affected general development, especially resulting in defective head organs and reduced body axis length. Our results show that the monoallelic p.K91E substitution on HIST1H4J underlies a human syndrome that is genetically and phenotypically akin to the HIST1H4C-associated neurodevelopmental disorder resulting from p.K91A and p.K91Q substitions in HIST1H4C. The highly overlapping patient phenotypes highlight functional similarities between HIST1H4J and HIST1H4C perturbations, establishing the singular importance of K91 across histone H4 genes for vertebrate development.
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http://dx.doi.org/10.1038/s41431-019-0552-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171094PMC
May 2020

Digital necrosis in an infant with severe spinal muscular atrophy.

Neurol Genet 2019 Oct 23;5(5):e361. Epub 2019 Sep 23.

Department of Molecular and Human Genetics (D.C., P.M., J.C.S., S.R.L., M.F.W.), Baylor College of Medicine, Houston, TX; Texas Children's Hospital (P.M., S.R.L., M.F.W.), Houston, TX; Baylor Genetics (J.C.S.), Houston, TX; Section of Palliative Medicine (J.A.J.), Department of Pediatrics, Baylor College of Medicine, Houston TX; and Jan and Dan Duncan Neurological Research Institute (M.F.W.), Texas Children's Hospital, Houston, TX.

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http://dx.doi.org/10.1212/NXG.0000000000000361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6807655PMC
October 2019

Disruptive variants of associate with autism and interfere with neuronal development and synaptic transmission.

Sci Adv 2019 09 25;5(9):eaax2166. Epub 2019 Sep 25.

Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.

RNA binding proteins are key players in posttranscriptional regulation and have been implicated in neurodevelopmental and neuropsychiatric disorders. Here, we report a significant burden of heterozygous, likely gene-disrupting variants in (encoding a highly constrained RNA binding protein) among patients with autism and related neurodevelopmental disabilities. Analysis of 17 patients identifies common phenotypes including autism, intellectual disability, language and motor delay, seizures, macrocephaly, and variable ocular abnormalities. HITS-CLIP revealed that Csde1-binding targets are enriched in autism-associated gene sets, especially FMRP targets, and in neuronal development and synaptic plasticity-related pathways. Csde1 knockdown in primary mouse cortical neurons leads to an overgrowth of the neurites and abnormal dendritic spine morphology/synapse formation and impaired synaptic transmission, whereas mutant and knockdown experiments in result in defects in synapse growth and synaptic transmission. Our study defines a new autism-related syndrome and highlights the functional role of CSDE1 in synapse development and synaptic transmission.
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http://dx.doi.org/10.1126/sciadv.aax2166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6760934PMC
September 2019

Loss of CLTRN function produces a neuropsychiatric disorder and a biochemical phenotype that mimics Hartnup disease.

Am J Med Genet A 2019 12 13;179(12):2459-2468. Epub 2019 Sep 13.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.

Hartnup disease is an autosomal recessive condition characterized by neutral aminoaciduria and behavioral problems. It is caused by a loss of B AT1, a neutral amino acid transporter in the kidney and intestine. CLTRN encodes the protein collectrin that functions in the transportation and activation of B AT1 in the renal apical brush bordered epithelium. Collectrin deficient mice have severe aminoaciduria. However, the phenotype associated with collectrin deficiency in humans has not been reported. Here we report two patients, an 11-year-old male who is hemizygous for a small, interstitial deletion on Xp22.2 that encompasses CLTRN and a 22-year-old male with a deletion spanning exons 1 to 3 of CLTRN. Both of them present with neuropsychiatric phenotypes including autistic features, anxiety, depression, compulsions, and motor tics, as well as neutral aminoaciduria leading to a clinical diagnosis of Hartnup disease and treatment with niacin supplementation. Plasma amino acids were normal in both patients. One patient had low 5-hydroxyindoleacetic acid levels, a serotoninergic metabolite. We explored the expression of collectrin in the murine brain and found it to be particularly abundant in the hippocampus, brainstem, and cerebellum. We propose that collectrin deficiency in humans can be associated with aminoaciduria and a clinical picture similar to that seen in Hartnup disease. Further studies are needed to explore the role of collectrin deficiency in the neurological phenotypes.
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http://dx.doi.org/10.1002/ajmg.a.61357DOI Listing
December 2019

Aberrant Function of the C-Terminal Tail of HIST1H1E Accelerates Cellular Senescence and Causes Premature Aging.

Am J Hum Genet 2019 09 22;105(3):493-508. Epub 2019 Aug 22.

Department of Psychiatry, University of Pretoria, Weskoppies Hospital, Pretoria, 0001 South Africa.

Histones mediate dynamic packaging of nuclear DNA in chromatin, a process that is precisely controlled to guarantee efficient compaction of the genome and proper chromosomal segregation during cell division and to accomplish DNA replication, transcription, and repair. Due to the important structural and regulatory roles played by histones, it is not surprising that histone functional dysregulation or aberrant levels of histones can have severe consequences for multiple cellular processes and ultimately might affect development or contribute to cell transformation. Recently, germline frameshift mutations involving the C-terminal tail of HIST1H1E, which is a widely expressed member of the linker histone family and facilitates higher-order chromatin folding, have been causally linked to an as-yet poorly defined syndrome that includes intellectual disability. We report that these mutations result in stable proteins that reside in the nucleus, bind to chromatin, disrupt proper compaction of DNA, and are associated with a specific methylation pattern. Cells expressing these mutant proteins have a dramatically reduced proliferation rate and competence, hardly enter into the S phase, and undergo accelerated senescence. Remarkably, clinical assessment of a relatively large cohort of subjects sharing these mutations revealed a premature aging phenotype as a previously unrecognized feature of the disorder. Our findings identify a direct link between aberrant chromatin remodeling, cellular senescence, and accelerated aging.
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http://dx.doi.org/10.1016/j.ajhg.2019.07.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731364PMC
September 2019

Loss-of-function mutations in Lysyl-tRNA synthetase cause various leukoencephalopathy phenotypes.

Neurol Genet 2019 Apr 18;5(2):e565. Epub 2019 Apr 18.

Department of Neurology (C.S., J.S., C.Z., J. Lu, J.X., S. Luo, J. Lin), Huashan Hospital, Fudan University, Shanghai, China; Baylor Genetic Laboratories (Y.J., Z.N., M.L.L., M.W., R.E.P., H.M., Y.Y.), Houston, TX; Department of Radiology (Y.L.), Huashan Hospital, Fudan University; Department of Pathology (Y.W., M.G.), Huashan Hospital, Fudan University, Shanghai, China; Department of Biochemistry and Molecular Pharmacology (M.L., K.D., Y.-M.H.), Thomas Jefferson University, Philadelphia, PA; Department of Human Genetics (S.N.O., A.A.), University of Michigan Medical School, Ann Arbor, MI; Department of Pediatrics and Department of Obstetrics and Gynecology (S.L.), University of Hawaii School of Medicine, Honolulu, HI; Department of Medical Oncology and Therapeutics Research (T.P.S.), Division of Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, CA; Department of Molecular and Human Genetics (P.L.M., A.L.M., L.E., S.R.L., Z.N., M.L.L., J.A.R., M.W., R.E.P., H.M., J.A.R., Y.Y., V.W.Z.), Baylor College of Medicine, Houston, TX; and AmCare Genomics Lab (V.W.Z.), Guangzhou, China.

Objective: To expand the clinical spectrum of lysyl-tRNA synthetase () gene-related diseases, which so far includes Charcot-Marie-Tooth disease, congenital visual impairment and microcephaly, and nonsyndromic hearing impairment.

Methods: Whole-exome sequencing was performed on index patients from 4 unrelated families with leukoencephalopathy. Candidate pathogenic variants and their cosegregation were confirmed by Sanger sequencing. Effects of mutations on KARS protein function were examined by aminoacylation assays and yeast complementation assays.

Results: Common clinical features of the patients in this study included impaired cognitive ability, seizure, hypotonia, ataxia, and abnormal brain imaging, suggesting that the CNS involvement is the main clinical presentation. Six previously unreported and 1 known mutations were identified and cosegregated in these families. Two patients are compound heterozygous for missense mutations, 1 patient is homozygous for a missense mutation, and 1 patient harbored an insertion mutation and a missense mutation. Functional and structural analyses revealed that these mutations impair aminoacylation activity of lysyl-tRNA synthetase, indicating that defective KARS function is responsible for the phenotypes in these individuals.

Conclusions: Our results demonstrate that patients with loss-of-function mutations can manifest CNS disorders, thus broadening the phenotypic spectrum associated with KARS-related disease.
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http://dx.doi.org/10.1212/NXG.0000000000000316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6515944PMC
April 2019

2-Pyrrolidinone and Succinimide as Clinical Screening Biomarkers for GABA-Transaminase Deficiency: Anti-seizure Medications Impact Accurate Diagnosis.

Front Neurosci 2019 8;13:394. Epub 2019 May 8.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.

Broad-scale untargeted biochemical phenotyping is a technology that supplements widely accepted assays, such as organic acid, amino acid, and acylcarnitine analyses typically utilized for the diagnosis of inborn errors of metabolism. In this study, we investigate the analyte changes associated with 4-aminobutyrate aminotransferase (ABAT, GABA transaminase) deficiency and treatments that affect GABA metabolism. GABA-transaminase deficiency is a rare neurodevelopmental and neurometabolic disorder caused by mutations in and resulting in accumulation of GABA in the cerebrospinal fluid (CSF). For that reason, measurement of GABA in CSF is currently the primary approach to diagnosis. GABA-transaminase deficiency results in severe developmental delay with intellectual disability, seizures, and movement disorder, and is often associated with death in childhood. Using an untargeted metabolomics platform, we analyzed EDTA plasma, urine, and CSF specimens from four individuals with GABA-transaminase deficiency to identify biomarkers by comparing the biochemical profile of individual patient samples to a pediatric-centric population cohort. Metabolomic analyses of over 1,000 clinical plasma samples revealed a rich source of biochemical information. Three out of four patients showed significantly elevated levels of the molecule 2-pyrrolidinone (-score ≥2) in plasma, and whole exome sequencing revealed variants of uncertain significance in . Additionally, these same patients also had elevated levels of succinimide in plasma, urine, and CSF and/or homocarnosine in urine and CSF. In the analysis of clinical EDTA plasma samples, the levels of succinimide and 2-pyrrolidinone showed a high level of correlation ( = 0.73), indicating impairment in GABA metabolism and further supporting the association with GABA-transaminase deficiency and the pathogenicity of the variants. Further analysis of metabolomic data across our patient population revealed the association of elevated levels of 2-pyrrolidinone with administration of vigabatrin, a commonly used anti-seizure medication and a known inhibitor of GABA-transaminase. These data indicate that anti-seizure medications may alter the biochemical and metabolomic data, potentially impacting the interpretation and diagnosis for the patient. Further, these data demonstrate the power of combining broad scale genotyping and phenotyping technologies to diagnose inherited neurometabolic disorders and support the use of metabolic phenotyping of plasma to screen for GABA-transaminase deficiency.
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http://dx.doi.org/10.3389/fnins.2019.00394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6517487PMC
May 2019

Review of the phenotypic spectrum associated with haploinsufficiency of MYRF.

Am J Med Genet A 2019 07 8;179(7):1376-1382. Epub 2019 May 8.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.

The myelin regulatory factor gene (MYRF) encodes a transcription factor that is widely expressed. There is increasing evidence that heterozygous loss-of-function variants in MYRF can lead to abnormal development of the heart, genitourinary tract, diaphragm, and lungs. Here, we searched a clinical database containing the results of 12,000 exome sequencing studies. We identified three previously unreported males with putatively deleterious variants in MYRF: one with a point mutation predicted to affect splicing and two with frameshift variants. In all cases where parental DNA was available, these variants were found to have arisen de novo. The phenotypes identified in these subjects included a variety of congenital heart defects (CHD) (hypoplastic left heart syndrome, scimitar syndrome, septal defects, and valvular anomalies), genitourinary anomalies (ambiguous genitalia, hypospadias, and cryptorchidism), congenital diaphragmatic hernia, and pulmonary hypoplasia. The phenotypes seen in our subjects overlap those described in individuals diagnosed with PAGOD syndrome [MIM# 202660], a clinically defined syndrome characterized by pulmonary artery and lung hypoplasia, agonadism, omphalocele, and diaphragmatic defects that can also be associated with hypoplastic left heart and scimitar syndrome. These cases provide additional evidence that haploinsufficiency of MYRF causes a genetic syndrome whose cardinal features include CHD, urogenital anomalies, congenital diaphragmatic hernia, and pulmonary hypoplasia. We also conclude that consideration should be given to screening individuals with PAGOD for pathogenic variants in MYRF, and that individuals with MYRF deficiency who survive the neonatal period should be monitored closely for developmental delay and intellectual disability.
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http://dx.doi.org/10.1002/ajmg.a.61182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557668PMC
July 2019

ZMIZ1 Variants Cause a Syndromic Neurodevelopmental Disorder.

Am J Hum Genet 2019 02 10;104(2):319-330. Epub 2019 Jan 10.

Cook Children's Medical Center, Fort Worth, TX 76102, USA.

ZMIZ1 is a coactivator of several transcription factors, including p53, the androgen receptor, and NOTCH1. Here, we report 19 subjects with intellectual disability and developmental delay carrying variants in ZMIZ1. The associated features include growth failure, feeding difficulties, microcephaly, facial dysmorphism, and various other congenital malformations. Of these 19, 14 unrelated subjects carried de novo heterozygous single-nucleotide variants (SNVs) or single-base insertions/deletions, 3 siblings harbored a heterozygous single-base insertion, and 2 subjects had a balanced translocation disrupting ZMIZ1 or involving a regulatory region of ZMIZ1. In total, we identified 13 point mutations that affect key protein regions, including a SUMO acceptor site, a central disordered alanine-rich motif, a proline-rich domain, and a transactivation domain. All identified variants were absent from all available exome and genome databases. In vitro, ZMIZ1 showed impaired coactivation of the androgen receptor. In vivo, overexpression of ZMIZ1 mutant alleles in developing mouse brains using in utero electroporation resulted in abnormal pyramidal neuron morphology, polarization, and positioning, underscoring the importance of ZMIZ1 in neural development and supporting mutations in ZMIZ1 as the cause of a rare neurodevelopmental syndrome.
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http://dx.doi.org/10.1016/j.ajhg.2018.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369415PMC
February 2019

Microdeletions excluding YWHAE and PAFAH1B1 cause a unique leukoencephalopathy: further delineation of the 17p13.3 microdeletion spectrum.

Genet Med 2019 07 20;21(7):1652-1656. Epub 2018 Dec 20.

Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.

Purpose: Brain malformations caused by 17p13.3 deletions include lissencephaly with deletions of the larger Miller-Dieker syndrome region or smaller deletions of only PAFAH1B1, white matter changes, and a distinct syndrome due to deletions including YWHAE and CRK but sparing PAFAH1B1. We sought to understand the significance of 17p13.3 deletions between the YWHAE/CRK and PAFAH1B1 loci.

Methods: We analyzed the clinical features of six individuals from five families with 17p13.3 deletions between and not including YWHAE/CRK and PAFAH1B1 identified among individuals undergoing clinical chromosomal microarray testing or research genome sequencing.

Results: Five individuals from four families had multifocal white matter lesions while a sixth had a normal magnetic resonance image. A combination of our individuals and a review of those in the literature with white matter changes and deletions in this chromosomal region narrows the overlapping region for this brain phenotype to ~345 kb, including 11 RefSeq genes, with RTN4RL1 haploinsufficiency as the best candidate for causing this phenotype.

Conclusion: While previous literature has hypothesized dysmorphic features and white matter changes related to YWHAE, our cohort contributes evidence to the presence of additional genetic changes within 17p13.3 required for proper brain development.
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http://dx.doi.org/10.1038/s41436-018-0358-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586530PMC
July 2019
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