NM_152564.5(VPS13B):c.11339T>C (p.Val3780Ala) AND Cohen syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 25, 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:: RCV001048520.2

Allele description [Variation Report for NM_152564.5(VPS13B):c.11339T>C (p.Val3780Ala)]

NM_152564.5(VPS13B):c.11339T>C (p.Val3780Ala)

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.11339T>C (p.Val3780Ala)

HGVS:

NC_000008.11:g.99868412T>C
NG_007098.2:g.860147T>C
NM_017890.5:c.11414T>C
NM_152564.5:c.11339T>CMANE SELECT
NP_060360.3:p.Val3805Ala
NP_060360.3:p.Val3805Ala
NP_689777.3:p.Val3780Ala
LRG_351t1:c.11414T>C
LRG_351:g.860147T>C
LRG_351p1:p.Val3805Ala
NC_000008.10:g.100880640T>C
NM_017890.4:c.11414T>C

Protein change:

V3780A

Links:

dbSNP: rs1817212364

NCBI 1000 Genomes Browser:

rs1817212364

Molecular consequence:

NM_017890.5:c.11414T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_152564.5:c.11339T>C - 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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Stenotrophomonas sp. VM7 16S ribosomal RNA gene, partial sequence
Stenotrophomonas sp. VM7 16S ribosomal RNA gene, partial sequence
gi|333827842|gb|JF717762.1|

Nucleotide
Sedum caeruleum (37)
Nucleotide
1,2-phenylacetyl-CoA epoxidase subunit PaaD [Burkholderia pseudomallei]
1,2-phenylacetyl-CoA epoxidase subunit PaaD [Burkholderia pseudomallei]
gi|490671220|ref|WP_004536209.1|

Protein
target of EGR1 protein 1 isoform X2 [Homo sapiens]
target of EGR1 protein 1 isoform X2 [Homo sapiens]
gi|2462502645|ref|XP_054190040.1|

Protein
PREDICTED: Homo sapiens target of EGR1, exonuclease (TOE1), transcript variant X...
PREDICTED: Homo sapiens target of EGR1, exonuclease (TOE1), transcript variant X5, mRNA
gi|2462502650|ref|XM_054334068.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001212531	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 25, 2019)	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

SCV001212531

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 25, 2019)

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, SCV001212531.1

#	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 valine with alanine at codon 3805 of the VPS13B protein (p.Val3805Ala). The valine residue is moderately conserved and there is a small physicochemical difference between valine and alanine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with VPS13B-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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: Sep 29, 2024

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