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NM_033380.3(COL4A5):c.382A>T (p.Lys128Ter) AND X-linked Alport syndrome

Germline classification:
Likely pathogenic (1 submission)
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:
RCV004577175.1

Allele description [Variation Report for NM_033380.3(COL4A5):c.382A>T (p.Lys128Ter)]

NM_033380.3(COL4A5):c.382A>T (p.Lys128Ter)

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.382A>T (p.Lys128Ter)
HGVS:
  • NC_000023.11:g.108568819A>T
  • NG_011977.2:g.133896A>T
  • NM_000495.5:c.382A>T
  • NM_033380.3:c.382A>TMANE SELECT
  • NP_000486.1:p.Lys128Ter
  • NP_203699.1:p.Lys128Ter
  • LRG_232t1:c.382A>T
  • LRG_232t2:c.382A>T
  • LRG_232:g.133896A>T
  • LRG_232p1:p.Lys128Ter
  • LRG_232p2:p.Lys128Ter
  • NC_000023.10:g.107812049A>T
Protein change:
K128*
Molecular consequence:
  • NM_000495.5:c.382A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_033380.3:c.382A>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV005061064Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical 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, SCV005061064.1

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

Description

The observed stop gained c.382A>T(p.Lys128Ter) variant, lying in splice region of COL4A5 gene has not been reported previously as a pathogenic variant nor a benign variant, to our knowledge. The c.382A>T variant is absent in gnomAD Exomes. This variant has not been submitted to the ClinVar database. The nucleotide change c.382A>T in COL4A5 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This sequence change creates a premature translational stop signal (p.Lys128Ter) in the COL4A5 gene. This variant is predicted to cause loss of normal protein function through protein truncation. 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: Jun 23, 2024