NM_000093.5(COL5A1):c.1194_1196delinsG (p.Asp398fs) AND Ehlers-Danlos syndrome, classic type, 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 26, 2019
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:: RCV002564002.10

Allele description [Variation Report for NM_000093.5(COL5A1):c.1194_1196delinsG (p.Asp398fs)]

NM_000093.5(COL5A1):c.1194_1196delinsG (p.Asp398fs)

Gene:

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

Variant type:

Indel

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_000093.5(COL5A1):c.1194_1196delinsG (p.Asp398fs)

HGVS:

NC_000009.12:g.134731525_134731527delinsG
NG_008030.1:g.94720_94722delinsG
NM_000093.5:c.1194_1196delinsGMANE SELECT
NM_001278074.1:c.1194_1196delinsG
NP_000084.3:p.Asp398fs
NP_001265003.1:p.Asp398fs
LRG_737t1:c.1194_1196delinsG
LRG_737t2:c.1194_1196delinsG
LRG_737:g.94720_94722delinsG
LRG_737p2:p.Asp398fs
NC_000009.11:g.137623371_137623373delinsG
NC_000009.11:g.137623371_137623373delinsG
NM_000093.4:c.1194_1196delinsG

Protein change:

D398fs

Links:

dbSNP: rs1834879370

NCBI 1000 Genomes Browser:

rs1834879370

Molecular consequence:

NM_000093.5:c.1194_1196delinsG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001278074.1:c.1194_1196delinsG - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

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platelet-activating factor acetylhydrolase IB subunit alpha [Otolemur garnettii]
platelet-activating factor acetylhydrolase IB subunit alpha [Otolemur garnettii]
gi|395853239|ref|XP_003799123.1|

Protein
PREDICTED: platelet-activating factor acetylhydrolase IB subunit alpha [Capra hi...
PREDICTED: platelet-activating factor acetylhydrolase IB subunit alpha [Capra hircus]
gi|548507498|ref|XP_005693383.1|

Protein
platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa [Hom...
platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa [Homo sapiens]
gi|119610942|gb|EAW90536.1||gnl|WGS |hCP46320

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001414470	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 26, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23587214, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001414470

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 26, 2019)

germline

clinical testing

PubMed (2)
[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

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

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001414470.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant is not present in population databases (ExAC no frequency). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in COL5A1 are known to be pathogenic (PMID: 23587214). This variant has not been reported in the literature in individuals with COL5A1-related conditions. This sequence change creates a premature translational stop signal (p.Asp398Glufs*8) in the COL5A1 gene. It is expected to result in an absent or disrupted protein product.

#	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: Oct 26, 2024

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