NM_001854.4(COL11A1):c.965C>T (p.Pro322Leu) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Dec 12, 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:: RCV003488432.1

Allele description [Variation Report for NM_001854.4(COL11A1):c.965C>T (p.Pro322Leu)]

NM_001854.4(COL11A1):c.965C>T (p.Pro322Leu)

Gene:

COL11A1:collagen type XI alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p21.1

Genomic location:

Preferred name:

NM_001854.4(COL11A1):c.965C>T (p.Pro322Leu)

HGVS:

NC_000001.11:g.103025546G>A
NG_008033.2:g.87951C>T
NM_001190709.2:c.848C>T
NM_001854.4:c.965C>TMANE SELECT
NM_080629.3:c.1001C>T
NM_080630.4:c.897+670C>T
NP_001177638.1:p.Pro283Leu
NP_001845.3:p.Pro322Leu
NP_542196.2:p.Pro334Leu
NC_000001.10:g.103491102G>A
NM_001854.3:c.965C>T
NR_134980.2:n.1309C>T

Protein change:

P283L

Links:

dbSNP: rs183130583

NCBI 1000 Genomes Browser:

rs183130583

Molecular consequence:

NM_080630.4:c.897+670C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001190709.2:c.848C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001854.4:c.965C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_080629.3:c.1001C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_134980.2:n.1309C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004240948	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Dec 12, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004240948

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Dec 12, 2023)

germline

clinical testing

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

Citation Link

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

Racial and ethnic disparities in diagnostic efficacy of comprehensive genetic testing for sensorineural hearing loss.

Florentine MM, Rouse SL, Stephans J, Conrad D, Czechowicz J, Matthews IR, Meyer AK, Nadaraja GS, Parikh R, Virbalas J, Weinstein JE, Chan DK.

Hum Genet. 2022 Apr;141(3-4):495-504. doi: 10.1007/s00439-021-02338-4. Epub 2021 Sep 13.

PubMed [citation]

PMID:: 34515852
PMCID:: PMC9035005

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004240948.1

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

Description

Variant summary: COL11A1 c.965C>T (p.Pro322Leu) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00017 in 1613352 control chromosomes, predominantly at a frequency of 0.0044 within the Latino subpopulation in the gnomAD database (v4). c.965C>T has been reported in the literature in one individual affected with sensorineural hearing loss (Florentine_2021). The report does not provide unequivocal conclusions about association of the variant with Stickler Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified this variant as uncertain significance (n=3) and likely benign (n=1). Based on the evidence outlined above, the variant was classified as likely benign.

#	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: Nov 3, 2024

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