NM_000393.5(COL5A2):c.4358G>A (p.Arg1453Gln) AND Ehlers-Danlos syndrome, classic type, 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 9, 2022
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:: RCV003114352.10

Allele description [Variation Report for NM_000393.5(COL5A2):c.4358G>A (p.Arg1453Gln)]

NM_000393.5(COL5A2):c.4358G>A (p.Arg1453Gln)

Gene:

COL5A2:collagen type V alpha 2 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q32.2

Genomic location:

Preferred name:

NM_000393.5(COL5A2):c.4358G>A (p.Arg1453Gln)

Other names:

p.R1453Q:CGG>CAG

HGVS:

NC_000002.12:g.189034212C>T
NG_011799.3:g.196090G>A
NM_000393.5:c.4358G>AMANE SELECT
NP_000384.2:p.Arg1453Gln
LRG_738t1:c.4358G>A
LRG_738:g.196090G>A
LRG_738p1:p.Arg1453Gln
NC_000002.11:g.189898938C>T
NG_011799.2:g.150668G>A
NM_000393.3:c.4358G>A

Protein change:

R1453Q

Links:

dbSNP: rs149064715

NCBI 1000 Genomes Browser:

rs149064715

Molecular consequence:

NM_000393.5:c.4358G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Ehlers-Danlos syndrome, classic type, 2 (EDSCL2)
Synonyms:: Ehlers-Danlos syndrome, type 2; Ehlers-Danlos syndrome type 2 (formerly)
Identifiers:: MONDO: MONDO:0019568; MedGen: C0268336; Orphanet: 287; Orphanet: 90318; OMIM: 130010

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003800117	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Uncertain significance (Mar 9, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003800117

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)

Uncertain significance
(Mar 9, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV003800117.2

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

Description

The COL5A2 c.4358G>A; p.Arg1453Gln variant (rs149064715), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 213130). This variant is found in the general population with an allele frequency of 0.012% (33/282,210 alleles) in the Genome Aggregation Database. The arginine at codon 1453 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.23). Due to limited information, the clinical significance of this variant is uncertain at this time.

#	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: Nov 24, 2024

ClinVar

Relating variation to medicine