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NM_152564.5(VPS13B):c.5360G>T (p.Ser1787Ile) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 9, 2017
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:
RCV000489122.2

Allele description [Variation Report for NM_152564.5(VPS13B):c.5360G>T (p.Ser1787Ile)]

NM_152564.5(VPS13B):c.5360G>T (p.Ser1787Ile)

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.5360G>T (p.Ser1787Ile)
HGVS:
  • NC_000008.11:g.99641950G>T
  • NG_007098.2:g.633685G>T
  • NM_017890.5:c.5435G>T
  • NM_152564.5:c.5360G>TMANE SELECT
  • NP_060360.3:p.Ser1812Ile
  • NP_689777.3:p.Ser1787Ile
  • LRG_351:g.633685G>T
  • NC_000008.10:g.100654178G>T
  • NM_017890.3:c.5435G>T
Protein change:
S1787I
Links:
dbSNP: rs1085307957
NCBI 1000 Genomes Browser:
rs1085307957
Molecular consequence:
  • NM_017890.5:c.5435G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152564.5:c.5360G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000577731GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Nov 9, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000577731.3

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

Description

The S1812I variant in the VPS13B gene has not been published as a pathogenic variant, nor has it been reported as a benign polymorphism to our knowledge. The S1812I 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. The S1812I variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. The S1812I variant is a strong candidate for a disease-causing variant, however the possibility it may be a rare benign variant cannot be excluded

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

Last Updated: Sep 17, 2022