NM_152564.5(VPS13B):c.19A>T (p.Thr7Ser) AND Cohen syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 1, 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:: RCV001245112.6

Allele description [Variation Report for NM_152564.5(VPS13B):c.19A>T (p.Thr7Ser)]

NM_152564.5(VPS13B):c.19A>T (p.Thr7Ser)

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.19A>T (p.Thr7Ser)

HGVS:

NC_000008.11:g.99013807A>T
NG_007098.2:g.5542A>T
NM_015243.3:c.19A>T
NM_017890.5:c.19A>T
NM_152564.5:c.19A>TMANE SELECT
NM_181661.3:c.19A>T
NP_056058.2:p.Thr7Ser
NP_060360.3:p.Thr7Ser
NP_689777.3:p.Thr7Ser
NP_858047.2:p.Thr7Ser
LRG_351t1:c.19A>T
LRG_351:g.5542A>T
NC_000008.10:g.100026035A>T
NM_017890.4:c.19A>T
NM_152564.4:c.19A>T
NR_047582.2:n.122A>T

Protein change:

T7S

Links:

dbSNP: rs1413120643

NCBI 1000 Genomes Browser:

rs1413120643

Molecular consequence:

NM_015243.3:c.19A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_017890.5:c.19A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_152564.5:c.19A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181661.3:c.19A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_047582.2:n.122A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001418380	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 1, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002079419	Natera, Inc.	no assertion criteria provided	Uncertain significance (Apr 15, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001418380

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 1, 2021)

germline

clinical testing

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

SCV002079419

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Apr 15, 2020)

germline

clinical testing

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001418380.4

#	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 threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 7 of the VPS13B protein (p.Thr7Ser). This variant is present in population databases (no rsID available, gnomAD 0.003%). 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: 969707). 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

From Natera, Inc., SCV002079419.1

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

#	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: May 19, 2024

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