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NM_033380.3(COL4A5):c.3002T>A (p.Leu1001Ter) AND X-linked Alport syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 15, 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:
RCV002308303.2

Allele description [Variation Report for NM_033380.3(COL4A5):c.3002T>A (p.Leu1001Ter)]

NM_033380.3(COL4A5):c.3002T>A (p.Leu1001Ter)

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.3002T>A (p.Leu1001Ter)
HGVS:
  • NC_000023.11:g.108624320T>A
  • NG_011977.2:g.189397T>A
  • NM_000495.5:c.3002T>A
  • NM_033380.3:c.3002T>AMANE SELECT
  • NP_000486.1:p.Leu1001Ter
  • NP_203699.1:p.Leu1001Ter
  • LRG_232t1:c.3002T>A
  • LRG_232t2:c.3002T>A
  • LRG_232:g.189397T>A
  • LRG_232p1:p.Leu1001Ter
  • LRG_232p2:p.Leu1001Ter
  • NC_000023.10:g.107867550T>A
Protein change:
L1001*
Molecular consequence:
  • NM_000495.5:c.3002T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_033380.3:c.3002T>A - 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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002601997Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))		Likely pathogenic
(Mar 15, 2022) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Myriad Genetics, Inc., SCV002601997.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

NM_000495.4(COL4A5):c.3002T>A(L1001*) is expected to be pathogenic in the context of X-linked Alport syndrome. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in COL4A5, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.

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

Last Updated: Aug 5, 2023