NC_000002.11:g.(?_189839216)_(190044330_?)del AND Ehlers-Danlos syndrome, type 4

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 7, 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:: RCV003119290.3

Allele description [Variation Report for NC_000002.11:g.(?_189839216)_(190044330_?)del]

NC_000002.11:g.(?_189839216)_(190044330_?)del

Genes:: COL3A1:collagen type III alpha 1 chain [Gene - OMIM - HGNC]
COL5A2:collagen type V alpha 2 chain [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 2q32.2
Genomic location:: Chr2: 189839216 - 190044330 (on Assembly GRCh37)
Preferred name:: NC_000002.11:g.(?_189839216)_(190044330_?)del
HGVS:: NC_000002.11:g.(?_189839216)_(190044330_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Ehlers-Danlos syndrome, type 4
Synonyms:: Ehlers-Danlos syndrome vascular type; Ehlers Danlos syndrome, ecchymotic type; Ehlers Danlos syndrome, arterial type; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0017314; MedGen: C0268338; Orphanet: 286; OMIM: 130050

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003790610	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 7, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24922459, 20648054, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003790610

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 7, 2022)

germline

clinical testing

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

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

Survival is affected by mutation type and molecular mechanism in vascular Ehlers-Danlos syndrome (EDS type IV).

Pepin MG, Schwarze U, Rice KM, Liu M, Leistritz D, Byers PH.

Genet Med. 2014 Dec;16(12):881-8. doi: 10.1038/gim.2014.72. Epub 2014 Jun 12.

PubMed [citation]

PMID:: 24922459

Hemizygous deletion of COL3A1, COL5A2, and MSTN causes a complex phenotype with aortic dissection: a lesson for and from true haploinsufficiency.

Meienberg J, Rohrbach M, Neuenschwander S, Spanaus K, Giunta C, Alonso S, Arnold E, Henggeler C, Regenass S, Patrignani A, Azzarello-Burri S, Steiner B, Nygren AO, Carrel T, Steinmann B, Mátyás G.

Eur J Hum Genet. 2010 Dec;18(12):1315-21. doi: 10.1038/ejhg.2010.105. Epub 2010 Jul 21.

PubMed [citation]

PMID:: 20648054
PMCID:: PMC3002852

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003790610.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the COL3A1 gene has been identified. Loss-of-function variants in COL3A1 are known to be pathogenic (PMID: 24922459). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. Isolated whole-gene deletions of COL3A1 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 20648054). For these reasons, this variant has been classified as Pathogenic.

#	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: Nov 11, 2023

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