Developmental Brain Disorder Gene Database

LoF Variant Gene

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AR

VPS13B

HGNC:2183 (protein-coding gene)

vacuolar protein sorting 13 homolog B

Unique Cases:
42
Disorders:
ID, ASD, EP, ADHD, CP
Last Updated:
November 4, 2024

Summary
Cases
Publications
External

Gene Summary:

DBD Genes Classification
VPS13B is a High Confidence candidate gene classified as Tier AR. AR genes have autosomal recessive inheritance.
Gene Function
Mediates the transfer of lipids between membranes at organelle contact sites (By similarity). Binds phosphatidylinositol 3- phosphate (By similarity). Functions as a tethering factor in the slow endocytic recycling pathway, to assist traffic between early and recycling endosomes (PubMed:24334764, PubMed:30962439, PubMed:32375900). Involved in the transport of proacrosomal vesicles to the nuclear dense lamina (NDL) during spermatid development (By similarity). Plays a role in the assembly of the ... (Source: Uniprot)
Previous symbols
CHS1, COH1
Alias symbols
BLTP5B
Chromosomal Location
8q22.2
Genomic Coordinates
GRCh37:chr8:100025494-100889814
GRCh38:chr8:99013274-99877580
Associated Disorders
Intellectual Disability, Autism, Epilepsy, Attention Deficit Hyperactivity Disorder, Cerebral Palsy

Predictive Scores:

HI Score (Decipher)

4.55

pLI (gnomAD)

0.00

LOEUF (gnomAD)

0.65

Classifications from External Sources:

SFARI Score (SFARI)

1

DDG2P Classification (DDG2P)

Definitive

ClinGen Classification (ClinGen)

Definitive1

GenCC Classification (GenCC)

Definitive4 Strong2 Supportive1

Publications:

Enomoto Y et. al., CNV analysis using whole exome sequencing identified biallelic CNVs of VPS13B in siblings with intellectual disability., Eur J Med Genet, 2020
Hashmi JA et. al., Homozygosity mapping and whole exome sequencing provide exact diagnosis of Cohen syndrome in a Saudi family., Brain Dev, 2020
Wiśniowiecka-Kowalnik B et. al., Application of custom-designed oligonucleotide array CGH in 145 patients with autistic spectrum disorders., Eur J Hum Genet, 2013
Charng WL et. al., Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate., BMC Med Genomics, 2016
Dillon OJ et. al., Exome sequencing has higher diagnostic yield compared to simulated disease-specific panels in children with suspected monogenic disorders., Eur J Hum Genet, 2018
Deciphering Developmental Disorders Study. et. al., Large-scale discovery of novel genetic causes of developmental disorders., Nature, 2015
Harripaul R et. al., Mapping autosomal recessive intellectual disability: combined microarray and exome sequencing identifies 26 novel candidate genes in 192 consanguineous families., Mol Psychiatry, 2018
Rafiq MA et. al., Novel VPS13B Mutations in Three Large Pakistani Cohen Syndrome Families Suggests a Baloch Variant with Autistic-Like Features., BMC Med Genet, 2015
Yu TW et. al., Using whole-exome sequencing to identify inherited causes of autism., Neuron, 2013
Lal D et. al., Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies., PLoS Genet, 2015
Hu H et. al., Genetics of intellectual disability in consanguineous families., Mol Psychiatry, 2019
Abu Diab A et. al., The combination of whole-exome sequencing and clinical analysis allows better diagnosis of rare syndromic retinal dystrophies., Acta Ophthalmol, 2019
Duplomb L et. al., Cohen syndrome is associated with major glycosylation defects., Hum Mol Genet, 2014
Riazuddin S et. al., Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability., Mol Psychiatry, 2017
Griswold AJ et. al., Targeted massively parallel sequencing of autism spectrum disorder-associated genes in a case control cohort reveals rare loss-of-function risk variants., Mol Autism, 2015
Gilissen C et. al., Genome sequencing identifies major causes of severe intellectual disability., Nature, 2014
Grozeva D et. al., Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability., Hum Mutat, 2015
Koehler K et. al., A novel homozygous nonsense mutation of VPS13B associated with previously unreported features of Cohen syndrome., Am J Med Genet A, 2020
Nouri N et. al., Clinical and genetic profile of children with unexplained intellectual disability/developmental delay and epilepsy., Epilepsy Res, 2021
Gillentine MA et. al., The importance of phase analysis in multiexon copy number variation detected by aCGH in autosomal recessive disorder loci., Am J Med Genet A, 2017
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NCBI: Gene

Integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
NCBI: Gene

Gene Reviews

An international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families.
Gene Reviews

DECIPHER

DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants. DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient.
DECIPHER

SFARI

SFARI Gene is an evolving online database designed to permit quick entrée into the genetics of autism, and to help researchers track the ever-expanding genetic risk factors that emerge in the literature.
SFARI

ClinGen

ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.
ClinGen

GenCC

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases.
GenCC

gnomAD

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
gnomAD
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