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NM_033380.3(COL4A5):c.1499G>T (p.Gly500Val) AND X-linked Alport syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 5, 2022
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003389145.1

Allele description [Variation Report for NM_033380.3(COL4A5):c.1499G>T (p.Gly500Val)]

NM_033380.3(COL4A5):c.1499G>T (p.Gly500Val)

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.1499G>T (p.Gly500Val)
HGVS:
  • NC_000023.11:g.108595584G>T
  • NG_011977.2:g.160661G>T
  • NM_000495.5:c.1499G>T
  • NM_033380.3:c.1499G>TMANE SELECT
  • NP_000486.1:p.Gly500Val
  • NP_203699.1:p.Gly500Val
  • LRG_232t1:c.1499G>T
  • LRG_232t2:c.1499G>T
  • LRG_232:g.160661G>T
  • LRG_232p1:p.Gly500Val
  • LRG_232p2:p.Gly500Val
  • NC_000023.10:g.107838814G>T
  • NG_011977.1:g.160661G>T
Protein change:
G500V
Links:
dbSNP: rs1569493670
NCBI 1000 Genomes Browser:
rs1569493670
Molecular consequence:
  • NM_000495.5:c.1499G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033380.3:c.1499G>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

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
SCV004100854Medical Genetics Department, Charles Nicolle Hospital Tunis
no assertion criteria provided
Likely pathogenic
(Sep 5, 2022) 		inheritedclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
North Africaninheritedyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Medical Genetics Department, Charles Nicolle Hospital Tunis, SCV004100854.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1North African1not providednot providedclinical testingnot provided

Description

DNA sequencing revealed a novel missense variant, Gly500Val, in a Tunisian family. This variant is located within the conserved GLY-X-Y triple helical domain of the COL4A5 gene. It has been identified in two males in a hemizygous state and in three females in a heterozygous state. In silico studies suggest that the Gly500Val variant is likely to be pathogenic. Notably, this novel variant was absent in control Tunisian samples. In summary, the Gly500Val novel variant meets our criteria for classification as likely pathogenic, based on segregation studies, its absence in control samples, and bioinformatic analysis

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Feb 20, 2024