NM_000088.4(COL1A1):c.1678G>A (p.Gly560Ser) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jun 27, 2024
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:: RCV000255844.12

Allele description [Variation Report for NM_000088.4(COL1A1):c.1678G>A (p.Gly560Ser)]

NM_000088.4(COL1A1):c.1678G>A (p.Gly560Ser)

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.1678G>A (p.Gly560Ser)

HGVS:

NC_000017.11:g.50194032C>T
NG_007400.1:g.12608G>A
NM_000088.4:c.1678G>AMANE SELECT
NP_000079.2:p.Gly560Ser
NP_000079.2:p.Gly560Ser
LRG_1t1:c.1678G>A
LRG_1:g.12608G>A
LRG_1p1:p.Gly560Ser
NC_000017.10:g.48271393C>T
NM_000088.3:c.1678G>A
NM_000088.4:c.1678G>A

Protein change:

G560S

Links:

dbSNP: rs67507747

NCBI 1000 Genomes Browser:

rs67507747

Molecular consequence:

NM_000088.4:c.1678G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000322325	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 27, 2024)	germline	clinical testing	Citation Link,
SCV000334706	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Sep 2, 2015)	germline	clinical testing	Citation Link,
SCV001832315	Blueprint Genetics	criteria provided, single submitter (Blueprint Genetics Variant Classification Scheme)	Pathogenic (Nov 30, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000322325

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jun 27, 2024)

germline

clinical testing

Citation Link,

SCV000334706

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Sep 2, 2015)

germline

clinical testing

Citation Link,

SCV001832315

Blueprint Genetics

criteria provided, single submitter

(Blueprint Genetics Variant Classification Scheme)

Pathogenic
(Nov 30, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000322325.11

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

Description

Occurs in the triple helical domain and replaces a glycine in a canonical Gly-X-Y repeat; missense substitution of a canonical glycine residue is expected to disrupt normal protein folding and function, and this is an established mechanism of disease (PMID: 34007986); Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(G382S) using alternate nomenclature; This variant is associated with the following publications: (PMID: 25944380, 36307859, 36709916, 37270749, 37880672, 34627339, 7691343, 17078022, 15741671, 22753364, 26432670, 26177859, 27510842, 30715774, 30692697, 30886339, 31299979, 32981126, 33939306, 28528406, 36140746, 34358384, 24668929, 34007986)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000334706.4

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

#	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		1	not provided	not provided	not provided

From Blueprint Genetics, SCV001832315.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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