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NM_001848.3(COL6A1):c.1056+1G>A AND Bethlem myopathy 1A

Germline classification:
Pathogenic/Likely pathogenic (5 submissions)
Last evaluated:
Nov 13, 2023
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:
RCV000018714.50

Allele description [Variation Report for NM_001848.3(COL6A1):c.1056+1G>A]

NM_001848.3(COL6A1):c.1056+1G>A

Gene:
COL6A1:collagen type VI alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.3
Genomic location:
Preferred name:
NM_001848.3(COL6A1):c.1056+1G>A
HGVS:
  • NC_000021.9:g.45990827G>A
  • NG_008674.1:g.14079G>A
  • NM_001848.3:c.1056+1G>AMANE SELECT
  • LRG_475:g.14079G>A
  • NC_000021.8:g.47410741G>A
Note:
NCBI staff reviewed the sequence information reported in PubMed 10419498 to determine the location of this allele on the current reference sequence.
Nucleotide change:
IVS14DS, G-A, +1
Links:
OMIM: 120220.0006; dbSNP: rs398123631
NCBI 1000 Genomes Browser:
rs398123631
Molecular consequence:
  • NM_001848.3:c.1056+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
1

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000038997OMIM
no assertion criteria provided
Pathogenic
(Oct 1, 2007)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV000656972Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Nov 13, 2023)
germlineclinical testing

PubMed (10)
[See all records that cite these PMIDs]

SCV001519042GeneReviews
no classification provided
not providedgermlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV002579076MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jun 21, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003922371Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 2, 2023)
germlinecuration

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only, curation

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Large genomic deletions: a novel cause of Ullrich congenital muscular dystrophy.

Foley AR, Hu Y, Zou Y, Yang M, Medne L, Leach M, Conlin LK, Spinner N, Shaikh TH, Falk M, Neumeyer AM, Bliss L, Tseng BS, Winder TL, Bönnemann CG.

Ann Neurol. 2011 Jan;69(1):206-11. doi: 10.1002/ana.22283.

PubMed [citation]
PMID:
21280092
PMCID:
PMC5154621
See all PubMed Citations (14)

Details of each submission

From OMIM, SCV000038997.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In a 32-year-old man with Bethlem myopathy (BTHLM1A; 158810), Lamande et al. (1999) identified a heterozygous G-to-A transition at the +1 position of intron 14 of the COL6A1 gene, which resulted in skipping of exon 14 and deletion of 18 amino acids from the triple-helical domain of the COL6A1 chain. The mutant COL6A1 chains associated intracellularly with COL6A2 (120240) and COL6A3 (120250) to form disulfide-bonded monomers, but further assembly into dimers and tetramers was prevented, and molecules containing the mutant chain were not secreted. This triple-helical deletion thus resulted in production of half the normal amount of collagen VI.

Pan et al. (2003) identified the IVS14+1G-A transition in a 6-year-old boy with a relatively mild congenital muscular dystrophy phenotype with distal joint hyperlaxity but no joint contractures characteristic Bethlem myopathy. Because the patient was young and could still develop contractures, Pan et al. (2003) concluded that his phenotype could be compatible with sporadic Bethlem myopathy.

Lucioli et al. (2005) identified the IVS14+1G-A mutation in 6 of 16 unrelated patients with Bethlem myopathy and mutations in the COL6A1 gene.

Baker et al. (2007) identified the IVS14+1G-A mutation in 2 additional patients with Bethlem myopathy. Studies showed undisulfide-bonded collagen VI in cell culture medium, suggesting that some structurally abnormal protein was secreted.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000656972.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (10)

Description

This sequence change affects a donor splice site in intron 14 of the COL6A1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in COL6A1 are known to be disease-causing for autosomal recessive COL6A1-related conditions (PMID: 21280092, 20976770). However, certain variants affecting donor or acceptor splice sites in the triple helical domain of COL6A1 are expected to result in in-frame exon skipping and have been reported to cause autosomal dominant COL6A1-related conditions (PMID: 18366090). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with autosomal dominant Bethlem myopathy (PMID: 10419498, 12840783, 15955946, 17886299, 25749816). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 17174). Studies have shown that disruption of this splice site results in skipping of exon 14, but is expected to preserve the integrity of the reading-frame (PMID: 10419498, 12840783). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV001519042.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

Common variant that results in exon 14 skipping

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From MGZ Medical Genetics Center, SCV002579076.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV003922371.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (2)

Description

The heterozygous c.1056+1G>A variant in COL6A1 was identified by our study in one individual with congenital myopathy. Trio exome analysis showed this variant to be de novo. The c.1056+1G>A variant in COL6A1 has been reported in 19 unrelated individuals with autosomal dominant COL6A1-related myopathy (PMID: 24271325, PMID: 29419890, PMID: 25749816, PMID: 15955946, PMID: 17886299, PMID: 10419498, PMID: 12840783) and segregated with disease in 18 affected relatives from six families (PMID: 25749816, PMID: 15955946). The number of reported affected individuals with this variant is greater than expected compared to non-affected individuals with this variant. This variant was previously found to be de novo in three individuals with paternity and maternity confirmed (PMID: 12840783, PMID: 29419890) and was assumed de novo in one individual but maternity and paternity have not been confirmed (PMID: 15955946). This variant has also been reported in ClinVar (Variation ID: 17174) and has been interpreted as pathogenic by multiple submitters. This variant was absent from large population studies. RT-PCR analysis performed on affected tissue shows evidence of altered splicing, with in-frame skipping of exon 14 (PMID: 17886299, PMID: 10419498). Two different nucleotide changes that also result in a splice donor variant at the same site, c.1056+1G>T and c.1056+1G>C, have been previously reported pathogenic (ClinVar Variation ID: 946468, 1322138), and the variant being assessed here, c.1056+1G>A, is predicted by SpliceAI to have a similar effect on splicing. This variant is located in the 5' splice region. Computational tools predict a splicing impact, though this information is not predictive enough to determine pathogenicity. There is an in-frame cryptic splice site 54 bases from the intron-exon boundary, providing evidence that this variant may delete 18 amino acids instead of causing loss of function. However, this information is not predictive enough to determine pathogenicity. Heterozygous loss of function of the COL6A1 gene is an established disease mechanism in autosomal dominant COL6A1-related myopathy. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant COL6A1-related myopathy. ACMG/AMP Criteria applied: PVS1_Moderate, PS1_Supporting, PS2, PS3_Moderate, PM2_Supporting, PM3_VeryStrong, PM6_Supporting, PP1_Strong (Richards 2015).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024