NM_004369.4(COL6A3):c.8670_8690dup (p.Thr2898_Ile2899insThrThrThrLysProValThr) AND Bethlem myopathy 1A

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 4, 2022
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:: RCV002786576.10

Allele description [Variation Report for NM_004369.4(COL6A3):c.8670_8690dup (p.Thr2898_Ile2899insThrThrThrLysProValThr)]

NM_004369.4(COL6A3):c.8670_8690dup (p.Thr2898_Ile2899insThrThrThrLysProValThr)

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.8670_8690dup (p.Thr2898_Ile2899insThrThrThrLysProValThr)

HGVS:

NC_000002.12:g.237336430_237336450dup
NG_008676.1:g.82778_82798dup
NG_098093.1:g.247_267dup
NM_004369.4:c.8670_8690dupMANE SELECT
NM_057164.3:c.8149_8169dup
NM_057165.3:c.8050_8070dup
NM_057166.5:c.6849_6869dup
NM_057167.4:c.8052_8072dup
NP_004360.2:p.Thr2898_Ile2899insThrThrThrLysProValThr
NP_004360.2:p.Thr2898_Ile2899insThrThrThrLysProValThr
NP_476505.2:p.Thr2731_Ile2732insThrThrThrLysProValThr
NP_476506.2:p.Thr2698_Ile2699insThrThrThrLysProValThr
NP_476507.3:p.Thr2291_Ile2292insThrThrThrLysProValThr
NP_476508.2:p.Thr2692_Ile2693insThrThrThrLysProValThr
LRG_473t1:c.8650_8670dup
LRG_473:g.82778_82798dup
LRG_473p1:p.Thr2898_Ile2899insThrThrThrLysProValThr
NC_000002.11:g.238245052_238245053insACAGGCTTTGTTGTGGTGGTT
NC_000002.11:g.238245073_238245093dup
NM_004369.3:c.8650_8670dup

Molecular consequence:

NM_057164.3:c.8149_8169dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_057165.3:c.8050_8070dup - inframe_indel - [Sequence Ontology: SO:0001820]
NM_004369.4:c.8670_8690dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_057166.5:c.6849_6869dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_057167.4:c.8052_8072dup - 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
SCV003033434	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 4, 2022)	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

SCV003033434

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 4, 2022)

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, SCV003033434.2

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

Description

Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with COL6A3-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.8670_8690dup, results in the insertion of 7 amino acid(s) of the COL6A3 protein (p.Thr2892_Thr2898dup), but otherwise preserves the integrity of the reading frame.

#	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: Oct 26, 2024

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