NM_000093.5(COL5A1):c.50CCCCGCTGCTGC[1] (p.Pro21_Leu24del) AND Ehlers-Danlos syndrome, classic type, 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 5, 2023
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:: RCV003865923.2

Allele description [Variation Report for NM_000093.5(COL5A1):c.50CCCCGCTGCTGC[1] (p.Pro21_Leu24del)]

NM_000093.5(COL5A1):c.50CCCCGCTGCTGC[1] (p.Pro21_Leu24del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_000093.5(COL5A1):c.50CCCCGCTGCTGC[1] (p.Pro21_Leu24del)

HGVS:

NC_000009.12:g.134642237CCCCGCTGCTGC[1]
NG_008030.1:g.5432CCCCGCTGCTGC[1]
NM_000093.5:c.50CCCCGCTGCTGC[1]MANE SELECT
NM_001278074.1:c.50CCCCGCTGCTGC[1]
NP_000084.3:p.Pro21_Leu24del
NP_000084.3:p.Pro21_Leu24del
NP_001265003.1:p.Pro21_Leu24del
LRG_737t1:c.50_61CCCCGCTGCTGC[1]
LRG_737t2:c.50CCCCGCTGCTGC[1]
LRG_737:g.5432CCCCGCTGCTGC[1]
LRG_737p1:p.Pro21_Leu24del
LRG_737p2:p.Pro21_Leu24del
NC_000009.11:g.137534083CCCCGCTGCTGC[1]
NC_000009.11:g.137534083_137534094del
NM_000093.4:c.50_61CCCCGCTGCTGC[1]

Molecular consequence:

NM_000093.5:c.50CCCCGCTGCTGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001278074.1:c.50CCCCGCTGCTGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

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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cytochrome c oxidase subunit 3, partial (mitochondrion) [Neurotrichus gibbsii hy...
cytochrome c oxidase subunit 3, partial (mitochondrion) [Neurotrichus gibbsii hyacinthinus]
gi|2316819662|gb|UYF11921.1|

Protein
uncharacterized protein [Arabidopsis thaliana]
uncharacterized protein [Arabidopsis thaliana]
Gene ID:832792

Gene
Uncharacterized protein family (UPF0041) [Arabidopsis thaliana]
Uncharacterized protein family (UPF0041) [Arabidopsis thaliana]
Gene ID:827120

Gene
WNK10 with no lysine (K) kinase 10 [Arabidopsis thaliana]
WNK10 with no lysine (K) kinase 10 [Arabidopsis thaliana]
Gene ID:842771

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004667579	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 5, 2023)	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

SCV004667579

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 5, 2023)

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

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004667579.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with COL5A1-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.62_73del, results in the deletion of 4 amino acid(s) of the COL5A1 protein (p.Pro21_Leu24del), but otherwise preserves the integrity of the reading frame.

#	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: Sep 29, 2024

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