NM_000088.4(COL1A1):c.4181A>G (p.Asn1394Ser) AND Osteogenesis imperfecta

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Aug 11, 2021
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:: RCV001123188.15

Allele description [Variation Report for NM_000088.4(COL1A1):c.4181A>G (p.Asn1394Ser)]

NM_000088.4(COL1A1):c.4181A>G (p.Asn1394Ser)

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.4181A>G (p.Asn1394Ser)

HGVS:

NC_000017.11:g.50185845T>C
NG_007400.1:g.20795A>G
NM_000088.4:c.4181A>GMANE SELECT
NP_000079.2:p.Asn1394Ser
NP_000079.2:p.Asn1394Ser
LRG_1t1:c.4181A>G
LRG_1:g.20795A>G
LRG_1p1:p.Asn1394Ser
NC_000017.10:g.48263206T>C
NM_000088.3:c.4181A>G

Protein change:

N1394S

Links:

dbSNP: rs147266928

NCBI 1000 Genomes Browser:

rs147266928

Molecular consequence:

NM_000088.4:c.4181A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Osteogenesis imperfecta (OI)
Identifiers:: MONDO: MONDO:0019019; MeSH: D010013; MedGen: C0029434; OMIM: PS166200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001281998	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25146735, 26235824 Citation Link,
SCV002564737	Genome Diagnostics Laboratory, The Hospital for Sick Children	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Aug 11, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001281998

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 27, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV002564737

Genome Diagnostics Laboratory, The Hospital for Sick Children

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Aug 11, 2021)

germline

clinical testing

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

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

Type I procollagen C-propeptide defects: study of genotype-phenotype correlation and predictive role of crystal structure.

Symoens S, Hulmes DJ, Bourhis JM, Coucke PJ, De Paepe A, Malfait F.

Hum Mutat. 2014 Nov;35(11):1330-41. doi: 10.1002/humu.22677. Epub 2014 Oct 18.

PubMed [citation]

PMID:: 25146735

Two Rare Mutations in the COL1A2 Gene Associate With Low Bone Mineral Density and Fractures in Iceland.

Styrkarsdottir U, Thorleifsson G, Eiriksdottir B, Gudjonsson SA, Ingvarsson T, Center JR, Nguyen TV, Eisman JA, Christiansen C, Thorsteinsdottir U, Sigurdsson G, Stefansson K.

J Bone Miner Res. 2016 Jan;31(1):173-9. doi: 10.1002/jbmr.2604. Epub 2015 Aug 29.

PubMed [citation]

PMID:: 26235824

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001281998.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as 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

From Genome Diagnostics Laboratory, The Hospital for Sick Children, SCV002564737.1

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

#	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 10, 2024

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