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NM_152564.5(VPS13B):c.11071G>A (p.Ala3691Thr) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Nov 8, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002313806.9

Allele description [Variation Report for NM_152564.5(VPS13B):c.11071G>A (p.Ala3691Thr)]

NM_152564.5(VPS13B):c.11071G>A (p.Ala3691Thr)

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.11071G>A (p.Ala3691Thr)
HGVS:
  • NC_000008.11:g.99861802G>A
  • NG_007098.2:g.853537G>A
  • NM_017890.5:c.11146G>A
  • NM_152564.4:c.11071G>A
  • NM_152564.5:c.11071G>AMANE SELECT
  • NP_060360.3:p.Ala3716Thr
  • NP_689777.3:p.Ala3691Thr
  • LRG_351t1:c.11146G>A
  • LRG_351t2:c.11071G>A
  • LRG_351:g.853537G>A
  • LRG_351p1:p.Ala3716Thr
  • NC_000008.10:g.100874030G>A
  • NM_017890.3:c.11146G>A
  • NM_017890.4:c.11146G>A
Protein change:
A3691T
Links:
dbSNP: rs142476821
NCBI 1000 Genomes Browser:
rs142476821
Molecular consequence:
  • NM_017890.5:c.11146G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152564.5:c.11071G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000849183Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Nov 8, 2021) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

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

Citations

PubMed

Using whole-exome sequencing to identify inherited causes of autism.

Yu TW, Chahrour MH, Coulter ME, Jiralerspong S, Okamura-Ikeda K, Ataman B, Schmitz-Abe K, Harmin DA, Adli M, Malik AN, D'Gama AM, Lim ET, Sanders SJ, Mochida GH, Partlow JN, Sunu CM, Felie JM, Rodriguez J, Nasir RH, Ware J, Joseph RM, Hill RS, et al.

Neuron. 2013 Jan 23;77(2):259-73. doi: 10.1016/j.neuron.2012.11.002.

PubMed [citation]
PMID:
23352163
PMCID:
PMC3694430

Details of each submission

From Ambry Genetics, SCV000849183.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Jan 13, 2025