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NM_000091.5(COL4A3):c.4793T>G (p.Leu1598Arg) AND Autosomal dominant Alport syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 15, 2018
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:
RCV001251486.3

Allele description [Variation Report for NM_000091.5(COL4A3):c.4793T>G (p.Leu1598Arg)]

NM_000091.5(COL4A3):c.4793T>G (p.Leu1598Arg)

Genes:
MFF-DT:MFF divergent transcript [Gene - HGNC]
COL4A3:collagen type IV alpha 3 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q36.3
Genomic location:
Preferred name:
NM_000091.5(COL4A3):c.4793T>G (p.Leu1598Arg)
HGVS:
  • NC_000002.12:g.227310813T>G
  • NG_011591.1:g.151249T>G
  • NM_000091.5:c.4793T>GMANE SELECT
  • NP_000082.2:p.Leu1598Arg
  • NP_000082.2:p.Leu1598Arg
  • LRG_230t1:c.4793T>G
  • LRG_230:g.151249T>G
  • LRG_230p1:p.Leu1598Arg
  • NC_000002.11:g.228175529T>G
  • NM_000091.4:c.4793T>G
Protein change:
L1598R
Links:
dbSNP: rs752452590
NCBI 1000 Genomes Browser:
rs752452590
Molecular consequence:
  • NM_000091.5:c.4793T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal dominant Alport syndrome (ATS3A)
Synonyms:
Alport syndrome dominant type; Renal failure and sensorineural hearing loss; Alport syndrome 3, autosomal dominant; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007086; MedGen: C5882663; Orphanet: 63; Orphanet: 88918; OMIM: 104200

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001427110Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(May 15, 2018)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot 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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV001427110.2

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

Description

A heterozygous missense variant, NM_000091.4(COL4A3):c.4793T>G, has been identified in exon 51 of 52 of the COL4A3 gene. The variant is predicted to result in a major amino acid change from leucine to arginine at position 1598 of the protein (NP_000082.2(COL4A3):p.(Leu1598Arg)). The leucine residue at this position has very high conservation (100 vertebrates, UCSC), and is located within the C4 domain. In silico predictions for this variant are consistently pathogenic (Polyphen, SIFT, CADD, Mutation Taster). The variant is present in the gnomAD database at a frequency of 0.005% (0 homozygotes). This variant has not been previously reported in clinical cases. Based on the information available at the time of curation, this variant has been classified as VARIANT of UNCERTAIN SIGNIFICANCE (VUS).

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

Last Updated: Jun 23, 2024