NM_000088.4(COL1A1):c.1695del (p.Gly566fs) AND Osteogenesis imperfecta type I

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 27, 2022
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:: RCV003022394.3

Allele description [Variation Report for NM_000088.4(COL1A1):c.1695del (p.Gly566fs)]

NM_000088.4(COL1A1):c.1695del (p.Gly566fs)

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.1695del (p.Gly566fs)

HGVS:

NC_000017.11:g.50194018del
NG_007400.1:g.12625del
NM_000088.4:c.1695delMANE SELECT
NP_000079.2:p.Gly566Aspfs
NP_000079.2:p.Gly566fs
LRG_1t1:c.1692del
LRG_1:g.12625del
LRG_1p1:p.Gly566Aspfs
NC_000017.10:g.48271376del
NC_000017.10:g.48271379del
NM_000088.3:c.1692delC

Protein change:

G566fs

Molecular consequence:

NM_000088.4:c.1695del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

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E3 ubiquitin-protein ligase ARIH2 isoform a [Mus musculus]
E3 ubiquitin-protein ligase ARIH2 isoform a [Mus musculus]
gi|1269612224|ref|NP_001344212.1|

Protein
Neea grandis (0)
GEO DataSets
olfactory receptor 7G2-like [Peromyscus leucopus]
olfactory receptor 7G2-like [Peromyscus leucopus]
gi|1929234139|ref|XP_028718106.2|

Protein
Mus musculus ariadne RBR E3 ubiquitin protein ligase 2 (Arih2), transcript varia...
Mus musculus ariadne RBR E3 ubiquitin protein ligase 2 (Arih2), transcript variant 1, mRNA
gi|2502274742|ref|NM_011790.6|

Nucleotide
JGI_CAAO1897.fwd NIH_XGC_tropTe5 Xenopus tropicalis cDNA clone IMAGE:7698742 5',...
JGI_CAAO1897.fwd NIH_XGC_tropTe5 Xenopus tropicalis cDNA clone IMAGE:7698742 5', mRNA sequence
gi|58721411|gnl|dbEST|27638572|gb|C 53.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003315629	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 27, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 7942841, 9295084, 9443882, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003315629

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 27, 2022)

germline

clinical testing

PubMed (4)
[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

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 (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003315629.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with COL1A1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly566Aspfs*14) 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).

#	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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