NM_000093.5(COL5A1):c.5141_5143del (p.Ser1714del) AND Ehlers-Danlos syndrome, classic type

delete

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 7, 2016
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:: RCV000457411.1

Allele description

NM_000093.5(COL5A1):c.5141_5143del (p.Ser1714del)

Genes:

COL5A1:collagen type V alpha 1 chain [Gene - OMIM - HGNC]
LOC101448202:uncharacterized LOC101448202 [Gene]

Variant type:

Deletion

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_000093.5(COL5A1):c.5141_5143del (p.Ser1714del)

HGVS:

NC_000009.12:g.134834975_134834977del
NG_008030.1:g.198170_198172del
NM_000093.5:c.5141_5143delMANE SELECT
NM_001278074.1:c.5141_5143del
NP_000084.3:p.Ser1714del
NP_001265003.1:p.Ser1714del
LRG_737t2:c.5141_5143del
LRG_737:g.198170_198172del
LRG_737p2:p.Ser1714del
NC_000009.11:g.137726821_137726823del
NM_000093.4:c.5141_5143delCCT

Protein change:

S1714del

Links:

dbSNP: rs1060502250

NCBI 1000 Genomes Browser:

rs1060502250

Molecular consequence:

NM_000093.5:c.5141_5143del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001278074.1:c.5141_5143del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Ehlers-Danlos syndrome, classic type (cEDS)
Identifiers:: MONDO: MONDO:0007522; MedGen: C4225429; Orphanet: 287

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000548986	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Nov 7, 2016)	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

SCV000548986

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Nov 7, 2016)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000548986.2

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

Description

This sequence change deletes 3 nucleotides from exon 65 of the COL5A1 mRNA (c.5141_5143delCCT). This leads to the deletion of 1 amino acid residue in the COL5A1 protein (p.Ser1714del) but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a COL5A1-related disease. Family studies have indicated that this variant was not present in the parents of an individual with classical Ehlers-Danlos syndrome, which suggests that it was de novo in that affected individual (Invitae). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown. In summary, this variant is a novel in-frame deletion with uncertain impact on protein function. Because it has been observed as arising de novo in an affected individual, it has been classified as Likely 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: Apr 23, 2022

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