NM_080680.3(COL11A2):c.4951G>T (p.Val1651Phe) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 5, 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:: RCV001878928.4

Allele description [Variation Report for NM_080680.3(COL11A2):c.4951G>T (p.Val1651Phe)]

NM_080680.3(COL11A2):c.4951G>T (p.Val1651Phe)

Gene:

COL11A2:collagen type XI alpha 2 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.32

Genomic location:

Preferred name:

NM_080680.3(COL11A2):c.4951G>T (p.Val1651Phe)

HGVS:

NC_000006.12:g.33164386C>A
NG_011589.1:g.33083G>T
NM_080679.3:c.4630G>T
NM_080680.2:c.4951G>T
NM_080680.3:c.4951G>TMANE SELECT
NM_080681.3:c.4693G>T
NP_542410.2:p.Val1544Phe
NP_542411.2:p.Val1651Phe
NP_542412.2:p.Val1565Phe
NC_000006.11:g.33132163C>A

Protein change:

V1544F

Links:

dbSNP: rs766589324

NCBI 1000 Genomes Browser:

rs766589324

Molecular consequence:

NM_080679.3:c.4630G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_080680.3:c.4951G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_080681.3:c.4693G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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bZIP transcription factor 1-B-like isoform X1 [Phoenix dactylifera]
bZIP transcription factor 1-B-like isoform X1 [Phoenix dactylifera]
gi|1964402576|ref|XP_017701809.2|

Protein
Vitis vinifera cultivar Pinot Noir 40024 chromosome 13
Vitis vinifera cultivar Pinot Noir 40024 chromosome 13
gi|2560044360|gb|CP126660.1|

Nucleotide
phycoerythrin alpha subunit, partial (plastid) [Callithamnion baileyi]
phycoerythrin alpha subunit, partial (plastid) [Callithamnion baileyi]
gi|165988323|gb|ABY77487.1|

Protein
proline-rich protein 3 [Rattus norvegicus]
proline-rich protein 3 [Rattus norvegicus]
gi|47087089|ref|NP_997709.1|

Protein
Gm13321 predicted gene 13321 [Mus musculus]
Gm13321 predicted gene 13321 [Mus musculus]
Gene ID:100504380

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002137912	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 5, 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

SCV002137912

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 5, 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, SCV002137912.3

#	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, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 1651 of the COL11A2 protein (p.Val1651Phe). 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. 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 not expected to disrupt COL11A2 protein function. ClinVar contains an entry for this variant (Variation ID: 1371300). This variant has not been reported in the literature in individuals affected with COL11A2-related conditions. This variant is not present in population databases (gnomAD 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

ClinVar

Relating variation to medicine