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NM_000088.4(COL1A1):c.2784del (p.Gly929fs) AND Osteogenesis imperfecta type I

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Dec 12, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000689473.7

Allele description

NM_000088.4(COL1A1):c.2784del (p.Gly929fs)

Gene:
COL1A1:collagen type I alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17q21.33
Genomic location:
Preferred name:
NM_000088.4(COL1A1):c.2784del (p.Gly929fs)
Other names:
p.(Gly929Alafs*179)
HGVS:
  • NC_000017.11:g.50189422del
  • NG_007400.1:g.17218del
  • NM_000088.4:c.2784delMANE SELECT
  • NP_000079.2:p.Gly929fs
  • NP_000079.2:p.Gly929fs
  • LRG_1t1:c.2784del
  • LRG_1:g.17218del
  • LRG_1p1:p.Gly929fs
  • NC_000017.10:g.48266783del
  • NM_000088.3:c.2784del
  • NM_000088.3:c.2784delT
  • NM_000088.4:c.2784delTMANE SELECT
Protein change:
G929fs
Links:
dbSNP: rs72653155
NCBI 1000 Genomes Browser:
rs72653155
Molecular consequence:
  • NM_000088.4:c.2784del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
3

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000817126Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Dec 12, 2023)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV004100674Center of Genomic medicine, Geneva, University Hospital of Geneva
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 26, 2023)
maternalclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
Europeanmaternalyes3not providednot providednot providednot providedclinical testing

Citations

PubMed

Osteogenesis imperfecta type I: molecular heterogeneity for COL1A1 null alleles of type I collagen.

Willing MC, Deschenes SP, Scott DA, Byers PH, Slayton RL, Pitts SH, Arikat H, Roberts EJ.

Am J Hum Genet. 1994 Oct;55(4):638-47.

PubMed [citation]
PMID:
7942841
PMCID:
PMC1918287

Ehlers-Danlos syndrome type VIIA and VIIB result from splice-junction mutations or genomic deletions that involve exon 6 in the COL1A1 and COL1A2 genes of type I collagen.

Byers PH, Duvic M, Atkinson M, Robinow M, Smith LT, Krane SM, Greally MT, Ludman M, Matalon R, Pauker S, Quanbeck D, Schwarze U.

Am J Med Genet. 1997 Oct 3;72(1):94-105.

PubMed [citation]
PMID:
9295084
See all PubMed Citations (6)

Details of each submission

From Invitae, SCV000817126.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Gly929Alafs*179) in the COL1A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL1A1 are known to be pathogenic (PMID: 7942841, 9295084, 9443882). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with osteogenesis imperfecta type I (PMID: 11317364). ClinVar contains an entry for this variant (Variation ID: 523942). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Center of Genomic medicine, Geneva, University Hospital of Geneva, SCV004100674.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1European3not providednot providedclinical testing PubMed (1)

Description

This variant (heterozygous) was identified in an affected male patient (age: 6 months), inherited from the affected mother and also present in his brother who is also affected.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot provided3not providednot providednot provided

Last Updated: Feb 20, 2024