NM_000088.4(COL1A1):c.779G>A (p.Gly260Asp) AND Osteogenesis imperfecta type I

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 5, 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:: RCV001890294.6

Allele description [Variation Report for NM_000088.4(COL1A1):c.779G>A (p.Gly260Asp)]

NM_000088.4(COL1A1):c.779G>A (p.Gly260Asp)

Genes:

LOC126862586:CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:48273702-48274901 [Gene]
COL1A1:collagen type I alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.33

Genomic location:

Preferred name:

NM_000088.4(COL1A1):c.779G>A (p.Gly260Asp)

HGVS:

NC_000017.11:g.50197035C>T
NG_007400.1:g.9605G>A
NM_000088.4:c.779G>AMANE SELECT
NP_000079.2:p.Gly260Asp
LRG_1:g.9605G>A
NC_000017.10:g.48274396C>T

Protein change:

G260D

Links:

dbSNP: rs1598299070

NCBI 1000 Genomes Browser:

rs1598299070

Molecular consequence:

NM_000088.4:c.779G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Osteogenesis imperfecta type I (OI1)
Synonyms:: OI, TYPE I; Osteogenesis imperfecta type 1; OI type 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008146; MedGen: C0023931; Orphanet: 666; OMIM: 166200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002153992	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 5, 2021)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 27509835, 7695699, 8218237, 19344236, 9016532, 17078022, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002153992

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 5, 2021)

germline

clinical testing

PubMed (7)
[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

DNA sequence analysis in 598 individuals with a clinical diagnosis of osteogenesis imperfecta: diagnostic yield and mutation spectrum.

Bardai G, Moffatt P, Glorieux FH, Rauch F.

Osteoporos Int. 2016 Dec;27(12):3607-3613. Epub 2016 Aug 11.

PubMed [citation]

PMID:: 27509835

Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution.

Bella J, Eaton M, Brodsky B, Berman HM.

Science. 1994 Oct 7;266(5182):75-81.

PubMed [citation]

PMID:: 7695699

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002153992.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This variant has been observed in individual(s) with clinical features of osteogenesis imperfecta (PMID: 27509835, Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with aspartic acid at codon 260 of the COL1A1 protein (p.Gly260Asp). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and aspartic acid. For these reasons, this variant has been classified as Pathogenic. This variant disrupts the triple helix domain of COL1A1. Glycine residues within the Gly-Xaa-Yaa repeats of the triple helix domain are required for the structure and stability of fibrillar collagens (PMID: 7695699, 8218237, 19344236). In COL1A1, variants affecting these glycine residues are significantly enriched in individuals with disease (PMID: 9016532, 17078022) compared to the general population (ExAC). 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 expected to disrupt COL1A1 protein function.

#	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

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