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NM_033380.3(COL4A5):c.638G>A (p.Gly213Glu) AND X-linked Alport syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 23, 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:
RCV003152810.1

Allele description [Variation Report for NM_033380.3(COL4A5):c.638G>A (p.Gly213Glu)]

NM_033380.3(COL4A5):c.638G>A (p.Gly213Glu)

Gene:
COL4A5:collagen type IV alpha 5 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq22.3
Genomic location:
Preferred name:
NM_033380.3(COL4A5):c.638G>A (p.Gly213Glu)
HGVS:
  • NC_000023.11:g.108577980G>A
  • NG_011977.2:g.143057G>A
  • NM_000495.5:c.638G>A
  • NM_033380.3:c.638G>AMANE SELECT
  • NP_000486.1:p.Gly213Glu
  • NP_203699.1:p.Gly213Glu
  • LRG_232t1:c.638G>A
  • LRG_232t2:c.638G>A
  • LRG_232:g.143057G>A
  • LRG_232p1:p.Gly213Glu
  • LRG_232p2:p.Gly213Glu
  • NC_000023.10:g.107821210G>A
  • NG_011977.1:g.143057G>A
Protein change:
G213E
Links:
dbSNP: rs104886066
NCBI 1000 Genomes Browser:
rs104886066
Molecular consequence:
  • NM_000495.5:c.638G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033380.3:c.638G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
X-linked Alport syndrome (ATS1)
Synonyms:
NEPHROPATHY AND DEAFNESS, X-LINKED; Alport syndrome 1, X-linked recessive; Alport Syndrome and Thin Basement Membrane Nephropathy
Identifiers:
MONDO: MONDO:0010520; MedGen: C4746986; Orphanet: 63; Orphanet: 88917; OMIM: 301050

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0038415213billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Feb 23, 2023) 		unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A two-tier approach to mutation detection in the COL4A5 gene for Alport syndrome.

King K, Flinter FA, Green PM.

Hum Mutat. 2006 Oct;27(10):1061.

PubMed [citation]
PMID:
16941480

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 3billion, SCV003841521.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.98; 3Cnet: 0.95). Same nucleotide change resulting in same amino acid change has been previously reported to be associated with COL4A5-related disorder (PMID: 16941480). Different missense changes at the same codon (p.Gly213Arg, p.Gly213Val) have been reported to be associated with COL4A5 related disorder (ClinVar ID: VCV000599058, VCV001066320). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024