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NM_152564.5(VPS13B):c.6473C>G (p.Ser2158Ter) AND Cohen syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 10, 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:
RCV002307247.2

Allele description [Variation Report for NM_152564.5(VPS13B):c.6473C>G (p.Ser2158Ter)]

NM_152564.5(VPS13B):c.6473C>G (p.Ser2158Ter)

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.6473C>G (p.Ser2158Ter)
HGVS:
  • NC_000008.11:g.99717189C>G
  • NG_007098.2:g.708924C>G
  • NM_017890.5:c.6548C>G
  • NM_152564.5:c.6473C>GMANE SELECT
  • NP_060360.3:p.Ser2183Ter
  • NP_060360.3:p.Ser2183Ter
  • NP_689777.3:p.Ser2158Ter
  • NP_689777.3:p.Ser2158Ter
  • LRG_351t1:c.6548C>G
  • LRG_351t2:c.6473C>G
  • LRG_351:g.708924C>G
  • LRG_351p1:p.Ser2183Ter
  • LRG_351p2:p.Ser2158Ter
  • NC_000008.10:g.100729417C>G
  • NM_017890.4:c.6548C>G
  • NM_152564.4:c.6473C>G
Protein change:
S2158*
Molecular consequence:
  • NM_017890.5:c.6548C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_152564.5:c.6473C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Cohen syndrome (COH1)
Synonyms:
Pepper syndrome; Cutis verticis gyrata, retinitis pigmentosa, and sensorineural deafness
Identifiers:
MONDO: MONDO:0008999; MedGen: C0265223; Orphanet: 193; OMIM: 216550

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002604718Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))		Likely pathogenic
(Dec 10, 2021) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Myriad Genetics, Inc., SCV002604718.2

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

Description

NM_017890.4(VPS13B):c.6548C>G(S2183*) is expected to be pathogenic in the context of Cohen syndrome. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in VPS13B, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.

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

Last Updated: Dec 24, 2022