VPS13B

vacuolar protein sorting 13 homolog B, the group of bridge-like lipid transfer protein family

Basic information

Region (hg38): 8:99013266-99877580

Previous symbols: [ "CHS1", "COH1" ]

Links

ENSG00000132549NCBI:157680OMIM:607817HGNC:2183Uniprot:Q7Z7G8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Cohen syndrome (Definitive), mode of inheritance: AR
  • Cohen syndrome (Definitive), mode of inheritance: AR
  • Cohen syndrome (Strong), mode of inheritance: AR
  • Cohen syndrome (Strong), mode of inheritance: AR
  • Cohen syndrome (Definitive), mode of inheritance: AR
  • Cohen syndrome (Supportive), mode of inheritance: AR
  • Cohen syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cohen syndromeARAllergy/Immunology/InfectiousThough the condition may be frequently recognizable, individuals can have recurrent infections, and antiinfectious prophlyaxis and treatment (including G-CSF for neutropenia), as well as early and aggressive treatment of infections may be beneficialAllergy/Immunology/Infectious; Craniofacial; Dental; Musculoskeletal; Neurologic; Ophthalmologic4717588; 671157; 7438489; 7246618; 7166592; 6705238; 3989828; 3656371; 3223494; 9266925; 10466416; 10964838; 12676892; 12730828; 15211651; 15025727; 15141358; 20683995; 20301655; 20921020; 24311531
The condition may be frequently recognizable due to characteristic features, including dysmorphisms

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VPS13B gene.

  • Cohen syndrome (372 variants)
  • not provided (46 variants)
  • Inborn genetic diseases (11 variants)
  • Retinitis pigmentosa (3 variants)
  • 9 conditions (2 variants)
  • 6 conditions (1 variants)
  • Abnormality of the nervous system (1 variants)
  • High myopia;Global developmental delay;Retinal dystrophy (1 variants)
  • 8 conditions (1 variants)
  • VPS13B-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS13B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
12
clinvar
1526
clinvar
9
clinvar
1547
missense
2
clinvar
1756
clinvar
39
clinvar
3
clinvar
1800
nonsense
143
clinvar
89
clinvar
4
clinvar
1
clinvar
1
clinvar
238
start loss
1
clinvar
1
frameshift
225
clinvar
121
clinvar
12
clinvar
1
clinvar
1
clinvar
360
inframe indel
2
clinvar
44
clinvar
46
splice donor/acceptor (+/-2bp)
24
clinvar
130
clinvar
2
clinvar
10
clinvar
1
clinvar
167
splice region
2
81
212
11
306
non coding
2
clinvar
1
clinvar
45
clinvar
628
clinvar
114
clinvar
790
Total 394 345 1876 2205 129

Highest pathogenic variant AF is 0.000256

Variants in VPS13B

This is a list of pathogenic ClinVar variants found in the VPS13B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
8-99013347-T-A Cohen syndrome Uncertain significance (Jan 12, 2018)361034
8-99013352-G-A Cohen syndrome Uncertain significance (Sep 23, 2021)1803855
8-99013353-C-G Cohen syndrome Uncertain significance (Jan 13, 2018)908283
8-99013787-A-G Inborn genetic diseases Uncertain significance (Mar 12, 2019)1798643
8-99013789-A-T Cohen syndrome Uncertain significance (Nov 08, 2022)2029081
8-99013791-G-A Abnormal brain morphology • Cohen syndrome • not specified Conflicting classifications of pathogenicity (Jan 29, 2024)402220
8-99013793-T-A Cohen syndrome Uncertain significance (Dec 23, 2021)2180780
8-99013794-G-T Cohen syndrome Likely benign (Dec 30, 2023)1112559
8-99013797-G-A Cohen syndrome Likely benign (Jun 28, 2023)2912646
8-99013806-A-C Cohen syndrome Likely benign (Aug 19, 2022)1104508
8-99013806-A-G Cohen syndrome Likely benign (Aug 03, 2021)729770
8-99013806-A-T Cohen syndrome • VPS13B-related disorder Likely benign (Jul 25, 2022)2013626
8-99013807-A-T Cohen syndrome • VPS13B-related disorder Uncertain significance (Oct 04, 2023)969707
8-99013810-C-G Cohen syndrome Uncertain significance (Feb 01, 2022)2086154
8-99013810-CC-A Cohen syndrome Likely pathogenic (-)56652
8-99013813-A-G VPS13B-related disorder Uncertain significance (Jun 05, 2024)3348257
8-99013819-A-T Cohen syndrome Uncertain significance (Jun 14, 2022)2006593
8-99013823-G-A Inborn genetic diseases Uncertain significance (Oct 30, 2023)3188776
8-99013824-C-T Cohen syndrome Likely benign (Mar 23, 2023)2848749
8-99013825-T-C not specified Uncertain significance (Aug 17, 2015)437252
8-99013844-A-G Cohen syndrome • Inborn genetic diseases • VPS13B-related disorder Uncertain significance (Jun 13, 2022)195336
8-99013848-C-A Cohen syndrome Uncertain significance (Aug 09, 2022)1438146
8-99013851-A-G Cohen syndrome Likely benign (Nov 19, 2020)1130880
8-99013857-G-A Cohen syndrome Likely benign (Oct 22, 2023)1153924
8-99013857-G-C Cohen syndrome Likely benign (Sep 17, 2022)1112932

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
VPS13Bprotein_codingprotein_codingENST00000358544 61864315
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.50e-451.0012535203961257480.00158
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.98219472.07e+30.9390.00010726435
Missense in Polyphen340406.80.835794958
Synonymous-0.6267727501.030.00003967801
Loss of Function5.711051900.5530.000009942298

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002610.00259
Ashkenazi Jewish0.001790.00179
East Asian0.001640.00163
Finnish0.003530.00352
European (Non-Finnish)0.001480.00146
Middle Eastern0.001640.00163
South Asian0.001450.00144
Other0.0006530.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: May be involved in protein sorting in post Golgi membrane traffic. {ECO:0000250}.;

Recessive Scores

pRec
0.176

Intolerance Scores

loftool
0.933
rvis_EVS
-0.61
rvis_percentile_EVS
17.5

Haploinsufficiency Scores

pHI
0.284
hipred
Y
hipred_score
0.544
ghis
0.600

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.349

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Vps13b
Phenotype

Gene ontology

Biological process
protein transport
Cellular component
Molecular function