NM_004369.4(COL6A3):c.3902G>A (p.Arg1301Gln) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Dec 11, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000725141.18

Allele description [Variation Report for NM_004369.4(COL6A3):c.3902G>A (p.Arg1301Gln)]

NM_004369.4(COL6A3):c.3902G>A (p.Arg1301Gln)

Gene:

COL6A3:collagen type VI alpha 3 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q37.3

Genomic location:

Preferred name:

NM_004369.4(COL6A3):c.3902G>A (p.Arg1301Gln)

HGVS:

NC_000002.12:g.237372115C>T
NG_008676.1:g.47093G>A
NM_004369.4:c.3902G>AMANE SELECT
NM_057164.5:c.2681G>A
NM_057165.5:c.3284G>A
NM_057166.5:c.2081G>A
NM_057167.4:c.3284G>A
NP_004360.2:p.Arg1301Gln
NP_004360.2:p.Arg1301Gln
NP_476505.3:p.Arg894Gln
NP_476506.3:p.Arg1095Gln
NP_476507.3:p.Arg694Gln
NP_476508.2:p.Arg1095Gln
LRG_473t1:c.3902G>A
LRG_473:g.47093G>A
LRG_473p1:p.Arg1301Gln
NC_000002.11:g.238280758C>T
NM_004369.3:c.3902G>A

Protein change:

R1095Q

Links:

dbSNP: rs148038440

NCBI 1000 Genomes Browser:

rs148038440

Molecular consequence:

NM_004369.4:c.3902G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_057164.5:c.2681G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_057165.5:c.3284G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_057166.5:c.2081G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_057167.4:c.3284G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000334397	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Oct 4, 2017)	germline	clinical testing	Citation Link,
SCV000590000	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Nov 18, 2019)	germline	clinical testing	Citation Link,
SCV003828272	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Dec 11, 2023)	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

SCV000334397

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Oct 4, 2017)

germline

clinical testing

Citation Link,

SCV000590000

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Nov 18, 2019)

germline

clinical testing

Citation Link,

SCV003828272

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Dec 11, 2023)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	7	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Eurofins Ntd Llc (ga), SCV000334397.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	7	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		7	not provided	not provided	not provided

From GeneDx, SCV000590000.4

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

Description

In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Reported as heterozygous variant in individual with reported clinically-suspected limb-girdle muscular dystrophy; however, a second variant in COL6A3 was not identified and additional clinical information was not provided (Nallamilli et al., 2018); This variant is associated with the following publications: (PMID: 30564623)

#	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 Revvity Omics, Revvity, SCV003828272.2

#	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: Apr 20, 2024

ClinVar

Relating variation to medicine