NM_198239.2(CCN6):c.1000T>A (p.Ser334Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 24, 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:: RCV002236536.6

Allele description [Variation Report for NM_198239.2(CCN6):c.1000T>A (p.Ser334Thr)]

NM_198239.2(CCN6):c.1000T>A (p.Ser334Thr)

Gene:

CCN6:cellular communication network factor 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q21

Genomic location:

Preferred name:

NM_198239.2(CCN6):c.1000T>A (p.Ser334Thr)

HGVS:

NC_000006.12:g.112069555T>A
NG_011748.1:g.20481T>A
NM_003880.4:c.1000T>A
NM_198239.2:c.1000T>AMANE SELECT
NP_003871.1:p.Ser334Thr
NP_937882.2:p.Ser334Thr
NC_000006.11:g.112390758T>A
NR_125353.2:n.1318T>A
NR_125354.3:n.1145T>A

Protein change:

S334T

Links:

dbSNP: rs121908903

NCBI 1000 Genomes Browser:

rs121908903

Molecular consequence:

NM_003880.4:c.1000T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_198239.2:c.1000T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_125353.2:n.1318T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_125354.3:n.1145T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Herbaspirillum seropedicae strain AU14040, complete genome
Herbaspirillum seropedicae strain AU14040, complete genome
gi|1062756882|gb|CP013136.1|

Nucleotide
cytochrome oxidase subunit 1, partial (mitochondrion) [Phosichthys argenteus]
cytochrome oxidase subunit 1, partial (mitochondrion) [Phosichthys argenteus]
gi|343223975|gb|AEM15229.1|

Protein
cytochrome c oxidase subunit 1, partial (mitochondrion) [Phosichthys argenteus]
cytochrome c oxidase subunit 1, partial (mitochondrion) [Phosichthys argenteus]
gi|1799641184|gb|QHN64163.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002508114	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 24, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15631777, 22685593, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002508114

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 24, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

[Pathology and molecular pathogenesis of spondyloepiphyseal dysplasia tarda with progressive arthropathy caused by compound CCN6 heterogeneous gene mutations].

Peng YQ, Liao EY, Gu HM, Wei QY, Zhou HD, Li J, Xie H, Zhai MX, Tan LH, Luo XH, Wu XP, Hu PA, Ni JD, Su X, Jiang Y, Dai RC, Guo LJ, Yuan LQ, Wang M, Wang PF, Liu SP, Yang Y, et al.

Zhonghua Yi Xue Za Zhi. 2004 Nov 2;84(21):1796-803. Chinese.

PubMed [citation]

PMID:: 15631777

Novel and recurrent mutations of WISP3 in two Chinese families with progressive pseudorheumatoid dysplasia.

Sun J, Xia W, He S, Zhao Z, Nie M, Li M, Jiang Y, Xing X, Wang O, Meng X, Zhou X.

PLoS One. 2012;7(6):e38643. doi: 10.1371/journal.pone.0038643. Epub 2012 Jun 7.

PubMed [citation]

PMID:: 22685593
PMCID:: PMC3369844

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002508114.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change replaces serine with threonine at codon 334 of the WISP3 protein (p.Ser334Thr). The serine residue is moderately conserved and there is a small physicochemical difference between serine and threonine. 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. This variant disrupts the p.Ser334 amino acid residue in WISP3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15631777, 22685593). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with WISP3-related conditions. This variant is not present in population databases (ExAC no frequency).

#	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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