NM_001844.5(COL2A1):c.2858del (p.Pro953fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 24, 2021
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:: RCV001950786.5

Allele description [Variation Report for NM_001844.5(COL2A1):c.2858del (p.Pro953fs)]

NM_001844.5(COL2A1):c.2858del (p.Pro953fs)

Gene:

COL2A1:collagen type II alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q13.11

Genomic location:

Preferred name:

NM_001844.5(COL2A1):c.2858del (p.Pro953fs)

HGVS:

NC_000012.12:g.47978638del
NG_008072.1:g.30869del
NM_001844.5:c.2858delMANE SELECT
NM_033150.3:c.2651del
NP_001835.3:p.Pro953fs
NP_149162.2:p.Pro884fs
NC_000012.11:g.48372417del
NC_000012.11:g.48372421del

Protein change:

P884fs

Links:

dbSNP: rs2136527926

NCBI 1000 Genomes Browser:

rs2136527926

Molecular consequence:

NM_001844.5:c.2858del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_033150.3:c.2651del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV002236785	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 24, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 20179744, 26626311, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002236785

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 24, 2021)

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

Stickler syndrome caused by COL2A1 mutations: genotype-phenotype correlation in a series of 100 patients.

Hoornaert KP, Vereecke I, Dewinter C, Rosenberg T, Beemer FA, Leroy JG, Bendix L, Björck E, Bonduelle M, Boute O, Cormier-Daire V, De Die-Smulders C, Dieux-Coeslier A, Dollfus H, Elting M, Green A, Guerci VI, Hennekam RC, Hilhorts-Hofstee Y, Holder M, Hoyng C, Jones KJ, et al.

Eur J Hum Genet. 2010 Aug;18(8):872-80. doi: 10.1038/ejhg.2010.23. Epub 2010 Feb 24. Erratum in: Eur J Hum Genet. 2010 Aug;18(8):881.

PubMed [citation]

PMID:: 20179744
PMCID:: PMC2987380

The expanding spectrum of COL2A1 gene variants IN 136 patients with a skeletal dysplasia phenotype.

Barat-Houari M, Dumont B, Fabre A, Them FT, Alembik Y, Alessandri JL, Amiel J, Audebert S, Baumann-Morel C, Blanchet P, Bieth E, Brechard M, Busa T, Calvas P, Capri Y, Cartault F, Chassaing N, Ciorca V, Coubes C, David A, Delezoide AL, Dupin-Deguine D, et al.

Eur J Hum Genet. 2016 Jul;24(7):992-1000. doi: 10.1038/ejhg.2015.250. Epub 2015 Dec 2.

PubMed [citation]

PMID:: 26626311
PMCID:: PMC5070901

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002236785.3

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

Description

This sequence change creates a premature translational stop signal (p.Pro953Leufs*75) in the COL2A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL2A1 are known to be pathogenic (PMID: 20179744). For these reasons, this variant has been classified as Pathogenic. This variant has been observed in individual(s) with Stickler syndrome, type I (PMID: 26626311). This variant is not present in population databases (ExAC 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: Apr 15, 2024

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