NM_000093.5(COL5A1):c.1502del (p.Pro501fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 18, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000490153.24

Allele description [Variation Report for NM_000093.5(COL5A1):c.1502del (p.Pro501fs)]

NM_000093.5(COL5A1):c.1502del (p.Pro501fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_000093.5(COL5A1):c.1502del (p.Pro501fs)

HGVS:

NC_000009.12:g.134750549del
NG_008030.1:g.113744del
NM_000093.5:c.1502delMANE SELECT
NM_001278074.1:c.1502del
NP_000084.3:p.Pro501fs
NP_001265003.1:p.Pro501fs
LRG_737t2:c.1502del
LRG_737:g.113744del
LRG_737p2:p.Pro501fs
NC_000009.11:g.137642395del
NM_000093.3:c.1502del
NM_000093.3:c.1502delC

Protein change:

P501fs

Links:

dbSNP: rs1085307855

NCBI 1000 Genomes Browser:

rs1085307855

Molecular consequence:

NM_000093.5:c.1502del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001278074.1:c.1502del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens Kv channel interacting protein 1 (KCNIP1), transcript variant 2, mR...
Homo sapiens Kv channel interacting protein 1 (KCNIP1), transcript variant 2, mRNA
gi|27886683|ref|NM_014592.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000577503	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jan 18, 2024)	germline	clinical testing	Citation Link,
SCV001246378	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Nov 1, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000577503

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jan 18, 2024)

germline

clinical testing

Citation Link,

SCV001246378

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Nov 1, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000577503.5

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

Description

Identified in a patient with a COL5A1-related phenotype referred for genetic testing at GeneDx, and in an individual with classical EDS in published literature (PMID: 22696272); Not observed at significant frequency in large population cohorts (gnomAD); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Published functional studies demonstrate that c.1502delC results in loss of protein from this allele through nonsense-mediated mRNA decay in fibroblasts from an individual with classical EDS (PMID: 22696272); This variant is associated with the following publications: (PMID: 22696272, 33498938)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001246378.26

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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