NM_000093.5(COL5A1):c.5314G>A (p.Glu1772Lys) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 3, 2022
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:: RCV001509381.6

Allele description [Variation Report for NM_000093.5(COL5A1):c.5314G>A (p.Glu1772Lys)]

NM_000093.5(COL5A1):c.5314G>A (p.Glu1772Lys)

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_000093.5(COL5A1):c.5314G>A (p.Glu1772Lys)

HGVS:

NC_000009.12:g.134835148G>A
NG_008030.1:g.198343G>A
NM_000093.5:c.5314G>AMANE SELECT
NM_001278074.1:c.5314G>A
NP_000084.3:p.Glu1772Lys
NP_000084.3:p.Glu1772Lys
NP_001265003.1:p.Glu1772Lys
LRG_737t1:c.5314G>A
LRG_737t2:c.5314G>A
LRG_737:g.198343G>A
LRG_737p1:p.Glu1772Lys
LRG_737p2:p.Glu1772Lys
NC_000009.11:g.137726994G>A
NM_000093.4:c.5314G>A
p.Glu1772Lys

Protein change:

E1772K

Links:

dbSNP: rs759042440

NCBI 1000 Genomes Browser:

rs759042440

Molecular consequence:

NM_000093.5:c.5314G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001278074.1:c.5314G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001716057	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 12, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003915277	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Oct 3, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001716057

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 12, 2020)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003915277

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Oct 3, 2022)

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	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV001716057.1

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

#	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		1	not provided	not provided	not provided

From GeneDx, SCV003915277.1

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not located in the triple helical region, where the majority of pathogenic missense variants occur (Symoens et al., 2012; HGMD); Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 22696272)

#	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

Last Updated: Jan 4, 2025

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