NM_152564.5(VPS13B):c.7366G>A (p.Val2456Ile) AND VPS13B-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 2, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003398677.6

Allele description [Variation Report for NM_152564.5(VPS13B):c.7366G>A (p.Val2456Ile)]

NM_152564.5(VPS13B):c.7366G>A (p.Val2456Ile)

Gene:

VPS13B:vacuolar protein sorting 13 homolog B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q22.2

Genomic location:

Preferred name:

NM_152564.5(VPS13B):c.7366G>A (p.Val2456Ile)

HGVS:

NC_000008.11:g.99776893G>A
NG_007098.2:g.768628G>A
NM_017890.5:c.7441G>A
NM_152564.4:c.7366G>A
NM_152564.5:c.7366G>AMANE SELECT
NP_060360.3:p.Val2481Ile
NP_689777.3:p.Val2456Ile
LRG_351t1:c.7441G>A
LRG_351t2:c.7366G>A
LRG_351:g.768628G>A
LRG_351p1:p.Val2481Ile
NC_000008.10:g.100789121G>A
NM_017890.3:c.7441G>A
NM_017890.4:c.7441G>A
Q7Z7G8:p.Val2481Ile

Protein change:

V2456I

Links:

UniProtKB: Q7Z7G8#VAR_069429; dbSNP: rs201963516

Molecular consequence:

NM_017890.5:c.7441G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152564.5:c.7366G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: VPS13B-related disorder
Synonyms:: VPS13B-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004119311	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Uncertain significance (Jul 2, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004119311

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Uncertain significance
(Jul 2, 2024)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004119311.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The VPS13B c.7366G>A variant is predicted to result in the amino acid substitution p.Val2456Ile. This variant, which is referred to as c.7441G>A (p.Val2481Ile) on an alternative transcript (NM_017890), has been reported in the homozygous state in an individual with severe intellectual disability (Table S9, de Ligt et al. 2012. PubMed ID: 23033978). However, several other homozygous variants in other genes were identified in this individual and it is not clear if this variant was contributing to the phenotypes. This variant is reported in 0.036% of alleles in individuals of African descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 7, 2026

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