NM_000090.4(COL3A1):c.2356G>A (p.Gly786Arg) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 4, 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:: RCV001093160.27

Allele description [Variation Report for NM_000090.4(COL3A1):c.2356G>A (p.Gly786Arg)]

NM_000090.4(COL3A1):c.2356G>A (p.Gly786Arg)

Genes:

LOC126806446:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:189866210-189867409 [Gene]
COL3A1:collagen type III alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q32.2

Genomic location:

Preferred name:

NM_000090.4(COL3A1):c.2356G>A (p.Gly786Arg)

Other names:

G619R

HGVS:

NC_000002.12:g.189001554G>A
NG_007404.1:g.32182G>A
NM_000090.4:c.2356G>AMANE SELECT
NP_000081.1:p.Gly786Arg
NP_000081.2:p.Gly786Arg
LRG_3t1:c.2356G>A
LRG_3:g.32182G>A
LRG_3p1:p.Gly786Arg
NC_000002.11:g.189866280G>A
NM_000090.3:c.2356G>A
P02461:p.Gly786Arg

Protein change:

GLY619ARG

Links:

UniProtKB: P02461#VAR_001782; OMIM: 120180.0002; dbSNP: rs113485686

NCBI 1000 Genomes Browser:

rs113485686

Molecular consequence:

NM_000090.4:c.2356G>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
SCV001250009	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jul 1, 2018)	germline	clinical testing	Citation Link,
SCV001805285	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 4, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001250009

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Jul 1, 2018)

germline

clinical testing

Citation Link,

SCV001805285

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 4, 2024)

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	3	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001250009.26

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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		3	not provided	not provided	not provided

From GeneDx, SCV001805285.4

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Occurs in the triple helical domain and replaces the glycine in the 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 (HGMD); Also known as p.(G619R); This variant is associated with the following publications: (PMID: 18043893, 25525159, 2243125, 30474650, 31126764, 24650746, 24399159, 9036918, 10706896)

#	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 20, 2024

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