NM_004369.4(COL6A3):c.8637_8654dup (p.2875KPVTTT[3]) AND Bethlem myopathy 1A

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 19, 2019
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:: RCV001065471.2

Allele description [Variation Report for NM_004369.4(COL6A3):c.8637_8654dup (p.2875KPVTTT[3])]

NM_004369.4(COL6A3):c.8637_8654dup (p.2875KPVTTT[3])

Gene:

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

Variant type:

Duplication

Cytogenetic location:

2q37.3

Genomic location:

Preferred name:

NM_004369.4(COL6A3):c.8637_8654dup (p.2875KPVTTT[3])

HGVS:

NC_000002.12:g.237336448_237336465dup
NG_008676.1:g.82745_82762dup
NM_004369.4:c.8637_8654dupMANE SELECT
NM_057166.5:c.6816_6833dup
NM_057167.4:c.8019_8036dup
NP_004360.2:p.2875KPVTTT[3]
NP_476507.3:p.2268KPVTTT[3]
NP_476508.2:p.2669KPVTTT[3]
LRG_473t1:c.8637_8654dup
LRG_473:g.82745_82762dup
NC_000002.11:g.238245091_238245108dup
NM_004369.3:c.8637_8654dup

Links:

dbSNP: rs1167608831

NCBI 1000 Genomes Browser:

rs1167608831

Molecular consequence:

NM_004369.4:c.8637_8654dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_057166.5:c.6816_6833dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_057167.4:c.8019_8036dup - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Name:: Bethlem myopathy 1A
Synonyms:: Myopathy, benign congenital, with contractures; Bethlem myopathy 1
Identifiers:: MONDO: MONDO:0024530; MedGen: CN029274; Orphanet: 610; OMIM: 158810

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001230429	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 19, 2019)	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

SCV001230429

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 19, 2019)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001230429.1

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

Description

This variant, c.8637_8654dup, results in the insertion of 6 amino acid(s) to the COL6A3 protein (p.Lys2881_Thr2886dup), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with COL6A3-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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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