NM_152564.5(VPS13B):c.11146C>T (p.Arg3716Trp) AND Cohen syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 4, 2022
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:: RCV000811695.3

Allele description [Variation Report for NM_152564.5(VPS13B):c.11146C>T (p.Arg3716Trp)]

NM_152564.5(VPS13B):c.11146C>T (p.Arg3716Trp)

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.11146C>T (p.Arg3716Trp)

HGVS:

NC_000008.11:g.99861877C>T
NG_007098.2:g.853612C>T
NM_017890.5:c.11221C>T
NM_152564.4:c.11146C>T
NM_152564.5:c.11146C>TMANE SELECT
NP_060360.3:p.Arg3741Trp
NP_060360.3:p.Arg3741Trp
NP_689777.3:p.Arg3716Trp
LRG_351t1:c.11221C>T
LRG_351t2:c.11146C>T
LRG_351:g.853612C>T
LRG_351p1:p.Arg3741Trp
NC_000008.10:g.100874105C>T
NM_017890.4:c.11221C>T

Protein change:

R3716W

Links:

dbSNP: rs773324603

NCBI 1000 Genomes Browser:

rs773324603

Molecular consequence:

NM_017890.5:c.11221C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_152564.5:c.11146C>T - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

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Carnegiella marthae voucher LBP 4199 23601 cytochrome b (cytb) gene, partial cds; mitochondrial
gi|301128317|gb|GQ339527.1|

Nucleotide
Carnegiella marthae voucher LBP 4199 23601 seven in absentia 1A (sina) gene, par...
Carnegiella marthae voucher LBP 4199 23601 seven in absentia 1A (sina) gene, partial cds
gi|296909839|gb|GQ339568.1|

Nucleotide
Oncaea mediterranea ECONME02 gene for 18S rRNA, partial sequence
Oncaea mediterranea ECONME02 gene for 18S rRNA, partial sequence
gi|1917123665|dbj|LC581907.1|

Nucleotide
methyltransferase/corrinoid binding protein, partial [Hyphomicrobium sp. TW28]
methyltransferase/corrinoid binding protein, partial [Hyphomicrobium sp. TW28]
gi|66474957|gb|AAY47008.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000951974	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 4, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000951974

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 4, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV000951974.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 3741 of the VPS13B protein (p.Arg3741Trp). This variant is present in population databases (rs773324603, gnomAD 0.01%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 655502). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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