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NM_152564.5(VPS13B):c.7247+2043_7403del AND Cohen syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 14, 2019
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:
RCV001234253.2

Allele description [Variation Report for NM_152564.5(VPS13B):c.7247+2043_7403del]

NM_152564.5(VPS13B):c.7247+2043_7403del

Genes:
LOC126860453:MED14-independent group 3 enhancer GRCh37_chr8:100782591-100783790 [Gene]
VPS13B:vacuolar protein sorting 13 homolog B [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
8q22.2
Genomic location:
Preferred name:
NM_152564.5(VPS13B):c.7247+2043_7403del
HGVS:
  • NC_000008.10:g.100781239_100789156del
  • NC_000008.11:g.99769013_99776930del
  • NG_007098.2:g.760748_768665del
  • NM_017890.5:c.7322+2043_7478del
  • NM_152564.5:c.7247+2043_7403delMANE SELECT
  • LRG_351t1:c.7322+2041_7476del
  • LRG_351:g.760748_768665del
  • NC_000008.10:g.100781241_100789158del
  • NM_017890.4:c.7322+2041_7476del
Molecular consequence:
  • NM_017890.5:c.7322+2043_7478del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_152564.5:c.7247+2043_7403del - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001406889Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Sep 14, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001406889.1

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

Description

This variant results in the deletion of part of exon 41 (c.7322+2041_7476del) of the VPS13B gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with VPS13B-related conditions. Loss-of-function variants in VPS13B are known to be pathogenic (PMID: 15141358, 16648375, 20461111). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Sep 29, 2024