NM_080680.3(COL11A2):c.4978C>T (p.Arg1660Cys) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Feb 27, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV003717216.3

Allele description [Variation Report for NM_080680.3(COL11A2):c.4978C>T (p.Arg1660Cys)]

NM_080680.3(COL11A2):c.4978C>T (p.Arg1660Cys)

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.4978C>T (p.Arg1660Cys)

HGVS:

NC_000006.12:g.33164359G>A
NG_011589.1:g.33110C>T
NG_107844.1:g.560G>A
NM_001424108.1:c.4798C>T
NM_001424109.1:c.4132C>T
NM_001424110.1:c.3952C>T
NM_001424111.1:c.3952C>T
NM_001424112.1:c.2932C>T
NM_080679.3:c.4657C>T
NM_080680.2:c.4978C>T
NM_080680.3:c.4978C>TMANE SELECT
NM_080681.3:c.4720C>T
NP_001411037.1:p.Arg1600Cys
NP_001411038.1:p.Arg1378Cys
NP_001411039.1:p.Arg1318Cys
NP_001411040.1:p.Arg1318Cys
NP_001411041.1:p.Arg978Cys
NP_542410.2:p.Arg1553Cys
NP_542411.2:p.Arg1660Cys
NP_542412.2:p.Arg1574Cys
NC_000006.11:g.33132136G>A

Protein change:

R1318C

Molecular consequence:

NM_001424108.1:c.4798C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001424109.1:c.4132C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001424110.1:c.3952C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001424111.1:c.3952C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001424112.1:c.2932C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_080679.3:c.4657C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_080680.3:c.4978C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_080681.3:c.4720C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004510956	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Sep 18, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005332673	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Feb 27, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004510956

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Sep 18, 2023)

germline

clinical testing

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

SCV005332673

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Feb 27, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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, SCV004510956.1

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

#	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 GeneDx, SCV005332673.1

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

Description

Has not been previously published as pathogenic or benign to our knowledge; Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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