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NM_000393.5(COL5A2):c.2130+1G>A AND Ehlers-Danlos syndrome, classic type, 1

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 6, 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:
RCV002040312.5

Allele description

NM_000393.5(COL5A2):c.2130+1G>A

Gene:
COL5A2:collagen type V alpha 2 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q32.2
Genomic location:
Preferred name:
NM_000393.5(COL5A2):c.2130+1G>A
HGVS:
  • NC_000002.12:g.189058848C>T
  • NG_011799.3:g.171454G>A
  • NM_000393.5:c.2130+1G>AMANE SELECT
  • LRG_738t1:c.2130+1G>A
  • LRG_738:g.171454G>A
  • NC_000002.11:g.189923574C>T
Links:
dbSNP: rs2105579086
NCBI 1000 Genomes Browser:
rs2105579086
Molecular consequence:
  • NM_000393.5:c.2130+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Ehlers-Danlos syndrome, classic type, 1 (EDSCL1)
Synonyms:
EHLERS-DANLOS SYNDROME, GRAVIS TYPE; EHLERS-DANLOS SYNDROME, SEVERE CLASSIC TYPE; Ehlers-Danlos syndrome, type 1; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0019567; MedGen: C0268335; OMIM: 130000

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002300341Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Dec 6, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

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

Clinical and molecular characterization of 40 patients with classic Ehlers-Danlos syndrome: identification of 18 COL5A1 and 2 COL5A2 novel mutations.

Ritelli M, Dordoni C, Venturini M, Chiarelli N, Quinzani S, Traversa M, Zoppi N, Vascellaro A, Wischmeijer A, Manfredini E, Garavelli L, Calzavara-Pinton P, Colombi M.

Orphanet J Rare Dis. 2013 Apr 12;8:58. doi: 10.1186/1750-1172-8-58.

PubMed [citation]
PMID:
23587214
PMCID:
PMC3653713
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002300341.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1508026). This variant has not been reported in the literature in individuals affected with COL5A2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 32 of the COL5A2 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 COL5A2 are known to be pathogenic (PMID: 23587214).

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

Last Updated: Mar 5, 2024