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NM_152564.5(VPS13B):c.6947A>G (p.Tyr2316Cys) AND VPS13B-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 5, 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:
RCV003905014.2

Allele description [Variation Report for NM_152564.5(VPS13B):c.6947A>G (p.Tyr2316Cys)]

NM_152564.5(VPS13B):c.6947A>G (p.Tyr2316Cys)

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.6947A>G (p.Tyr2316Cys)
HGVS:
  • NC_000008.11:g.99720944A>G
  • NG_007098.2:g.712679A>G
  • NM_017890.5:c.7022A>G
  • NM_152564.5:c.6947A>GMANE SELECT
  • NP_060360.3:p.Tyr2341Cys
  • NP_060360.3:p.Tyr2341Cys
  • NP_689777.3:p.Tyr2316Cys
  • LRG_351t1:c.7022A>G
  • LRG_351:g.712679A>G
  • LRG_351p1:p.Tyr2341Cys
  • NC_000008.10:g.100733172A>G
  • NM_017890.4:c.7022A>G
  • NM_152564.4:c.6947A>G
  • Q7Z7G8:p.Tyr2341Cys
Protein change:
Y2316C
Links:
UniProtKB: Q7Z7G8#VAR_038422; dbSNP: rs386834104
NCBI 1000 Genomes Browser:
rs386834104
Molecular consequence:
  • NM_017890.5:c.7022A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152564.5:c.6947A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004722705PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Uncertain significance
(Jun 5, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004722705.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The VPS13B c.6947A>G variant is predicted to result in the amino acid substitution p.Tyr2316Cys. The VPS13B gene was previously known as COH1 with this variant being described using alternative nomenclature of c.7022A>G (p.Tyr2341Cys). This variant was reported in the compound heterozygous state along with a truncating variant in a patient with Cohen syndrome (Hennies et al. 2004. PubMed ID: 15154116). This variant is reported in 0.0096% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 7, 2025