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NM_152564.5(VPS13B):c.1915C>T (p.Arg639Ter) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Nov 30, 2018
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000255734.7

Allele description [Variation Report for NM_152564.5(VPS13B):c.1915C>T (p.Arg639Ter)]

NM_152564.5(VPS13B):c.1915C>T (p.Arg639Ter)

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.1915C>T (p.Arg639Ter)
HGVS:
  • NC_000008.11:g.99147912C>T
  • NG_007098.2:g.139647C>T
  • NM_015243.3:c.1915C>T
  • NM_017890.5:c.1915C>T
  • NM_152564.5:c.1915C>TMANE SELECT
  • NP_056058.2:p.Arg639Ter
  • NP_060360.3:p.Arg639Ter
  • NP_060360.3:p.Arg639Ter
  • NP_689777.3:p.Arg639Ter
  • NP_689777.3:p.Arg639Ter
  • LRG_351t1:c.1915C>T
  • LRG_351t2:c.1915C>T
  • LRG_351:g.139647C>T
  • LRG_351p1:p.Arg639Ter
  • LRG_351p2:p.Arg639Ter
  • NC_000008.10:g.100160140C>T
  • NM_017890.3:c.1915C>T
  • NM_017890.4:c.1915C>T
  • NM_152564.4:c.1915C>T
Protein change:
R639*
Links:
dbSNP: rs764776104
NCBI 1000 Genomes Browser:
rs764776104
Molecular consequence:
  • NM_015243.3:c.1915C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_017890.5:c.1915C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_152564.5:c.1915C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000322116GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Nov 30, 2018) 		germlineclinical testing

Citation Link,

SCV000703985Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Pathogenic
(Dec 12, 2016) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000322116.7

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

Description

The R639X pathogenic variant in the VPS13B gene has been reported previously in a patient with Cohen syndrome including features of microcephaly, short stature, and truncal obesity. This individual was presumed compound heterozygous for this pathogenic variant and another protein truncating/loss-of-function variant; this patient also harbored a pathogenic variant in the ELANE gene, which was felt to be related to her severe neutropenia (Beene et al., 2015). The R639X variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R639X variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret R639X as a pathogenic variant.

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

From Eurofins Ntd Llc (ga), SCV000703985.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024