NM_198239.2(CCN6):c.1000T>C (p.Ser334Pro) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 15, 2023
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:: RCV003555946.2

Allele description [Variation Report for NM_198239.2(CCN6):c.1000T>C (p.Ser334Pro)]

NM_198239.2(CCN6):c.1000T>C (p.Ser334Pro)

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>C (p.Ser334Pro)

HGVS:

NC_000006.12:g.112069555T>C
NG_011748.1:g.20481T>C
NM_003880.4:c.1000T>C
NM_198239.2:c.1000T>CMANE SELECT
NP_003871.1:p.Ser334Pro
NP_937882.2:p.Ser334Pro
NC_000006.11:g.112390758T>C
NR_125353.2:n.1318T>C
NR_125354.3:n.1145T>C

Protein change:

S334P; SER334PRO

Links:

OMIM: 603400.0010; dbSNP: rs121908903

NCBI 1000 Genomes Browser:

rs121908903

Molecular consequence:

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

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Anaeromyxobacter dehalogenans 2CP-1 chromosome, complete genome
Anaeromyxobacter dehalogenans 2CP-1 chromosome, complete genome
gi|219952977|gb|CP001359.1|

Nucleotide
Agama 16S ribosomal RNA gene, partial sequence; mitochondrial.
Agama 16S ribosomal RNA gene, partial sequence; mitochondrial.
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004294671	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 15, 2023)	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

SCV004294671

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 15, 2023)

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, SCV004294671.1

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

Description

This missense change has been observed in individual(s) with progressive pseudorheumatoid dysplasia (PMID: 15631777, 22685593). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 334 of the WISP3 protein (p.Ser334Pro). This variant is not present in population databases (gnomAD no frequency). ClinVar contains an entry for this variant (Variation ID: 6388). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt WISP3 protein function. For these reasons, this variant has been classified as Pathogenic.

#	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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