NM_001286577.2(C2CD3):c.785A>T (p.Asn262Ile) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 21, 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:: RCV001918156.5

Allele description [Variation Report for NM_001286577.2(C2CD3):c.785A>T (p.Asn262Ile)]

NM_001286577.2(C2CD3):c.785A>T (p.Asn262Ile)

Genes:

C2CD3:C2 domain containing 3 centriole elongation regulator [Gene - OMIM - HGNC]
LOC121392929:Sharpr-MPRA regulatory region 9619 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.4

Genomic location:

Preferred name:

NM_001286577.2(C2CD3):c.785A>T (p.Asn262Ile)

HGVS:

NC_000011.10:g.74138890T>A
NG_041791.1:g.37130A>T
NG_074586.1:g.367T>A
NM_001286577.2:c.785A>TMANE SELECT
NM_015531.4:c.785A>T
NM_015531.6:c.785A>T
NP_001273506.1:p.Asn262Ile
NP_056346.3:p.Asn262Ile
NC_000011.9:g.73849935T>A

Protein change:

N262I

Links:

dbSNP: rs1440179602

NCBI 1000 Genomes Browser:

rs1440179602

Molecular consequence:

NM_001286577.2:c.785A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015531.6:c.785A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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photosystem I subunit IX (chloroplast) [Calophyllum inophyllum]
photosystem I subunit IX (chloroplast) [Calophyllum inophyllum]
gi|2328360605|ref|YP_010529100.1|

Protein
PREDICTED: Danio rerio si:ch211-266i6.3 (si:ch211-266i6.3), transcript variant X...
PREDICTED: Danio rerio si:ch211-266i6.3 (si:ch211-266i6.3), transcript variant X1, mRNA
gi|2800548113|ref|XM_692182.8|

Nucleotide
Mus musculus Rho GDP dissociation inhibitor alpha (Arhgdia), transcript variant ...
Mus musculus Rho GDP dissociation inhibitor alpha (Arhgdia), transcript variant 2, mRNA
gi|1390157430|ref|NM_001363425.1|

Nucleotide
Mus musculus single stranded DNA binding protein 4 (Ssbp4), transcript variant 7...
Mus musculus single stranded DNA binding protein 4 (Ssbp4), transcript variant 7, mRNA
gi|1733581505|ref|NM_133772.3|

Nucleotide
rho GDP-dissociation inhibitor 1 [Mus musculus]
rho GDP-dissociation inhibitor 1 [Mus musculus]
gi|31982030|ref|NP_598557.3|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002185779	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 21, 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

SCV002185779

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 21, 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, SCV002185779.2

#	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 asparagine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 262 of the C2CD3 protein (p.Asn262Ile). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with C2CD3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1406880). 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: "Possibly Damaging"; Align-GVGD: "Class C0"). 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

ClinVar

Relating variation to medicine