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NM_000393.5(COL5A2):c.1977G>A (p.Pro659=) AND Ehlers-Danlos syndrome, classic type, 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 18, 2024
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:
RCV002229088.8

Allele description [Variation Report for NM_000393.5(COL5A2):c.1977G>A (p.Pro659=)]

NM_000393.5(COL5A2):c.1977G>A (p.Pro659=)

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.1977G>A (p.Pro659=)
HGVS:
  • NC_000002.12:g.189062865C>T
  • NG_011799.3:g.167437G>A
  • NM_000393.5:c.1977G>AMANE SELECT
  • NP_000384.2:p.Pro659=
  • LRG_738t1:c.1977G>A
  • LRG_738:g.167437G>A
  • LRG_738p1:p.Pro659=
  • NC_000002.11:g.189927591C>T
  • NG_011799.2:g.122015G>A
  • NM_000393.3:c.1977G>A
Links:
dbSNP: rs863223491
NCBI 1000 Genomes Browser:
rs863223491
Molecular consequence:
  • NM_000393.5:c.1977G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000631574Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 18, 2024) 		germlineclinical testing

PubMed (5)
[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

A case of Ehlers-Danlos syndrome presenting with widened atrophic scars of forehead, elbow, knee, and pretibial area: A case report.

Xu X, Wang Z, Zan T.

Medicine (Baltimore). 2019 Sep;98(37):e17138. doi: 10.1097/MD.0000000000017138.

PubMed [citation]
PMID:
31517854
PMCID:
PMC6750314

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000631574.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change affects codon 659 of the COL5A2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the COL5A2 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with clinical features of COL5A2-related Ehlers-Danlos syndrome (PMID: 31517854, 33834621). In at least one individual the variant was observed to be de novo. This variant is also known as c.1997G>A. ClinVar contains an entry for this variant (Variation ID: 213101). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 29, but is expected to preserve the integrity of the reading-frame (PMID: 33834621). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 3, 2024