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NM_033380.3(COL4A5):c.2396-1G>A AND X-linked Alport syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 14, 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:
RCV003448718.2

Allele description [Variation Report for NM_033380.3(COL4A5):c.2396-1G>A]

NM_033380.3(COL4A5):c.2396-1G>A

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.2396-1G>A
HGVS:
  • NC_000023.11:g.108614910G>A
  • NG_011977.2:g.179987G>A
  • NM_000495.5:c.2396-1G>A
  • NM_033380.3:c.2396-1G>AMANE SELECT
  • LRG_232t1:c.2396-1G>A
  • LRG_232t2:c.2396-1G>A
  • LRG_232:g.179987G>A
  • NC_000023.10:g.107858140G>A
Links:
dbSNP: rs886041509
NCBI 1000 Genomes Browser:
rs886041509
Molecular consequence:
  • NM_000495.5:c.2396-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_033380.3:c.2396-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV004176366Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Feb 14, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical 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 Neuberg Centre For Genomic Medicine, NCGM, SCV004176366.1

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

Description

The invariant splice acceptor c.2396-1G>A variant in COL4A5 gene has been reported previously in hemizygous state in an individual affected Alport syndrome (Beicht et al. 2013). The c.2396-1G>A variant is novel (not in any individuals) in both gnomAD Exomes and 1000 Genomes databases. This variant has not been reported to the ClinVar database. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.

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

Last Updated: Apr 6, 2024