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NM_024426.6(WT1):c.500T>A (p.Val167Asp) AND Nephrotic syndrome, type 4

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 24, 2020
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:
RCV001093599.1

Allele description [Variation Report for NM_024426.6(WT1):c.500T>A (p.Val167Asp)]

NM_024426.6(WT1):c.500T>A (p.Val167Asp)

Genes:
WT1:WT1 transcription factor [Gene - OMIM - HGNC]
LOC107982234:WT1/WT1-AS bi-directional promoter region [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
11p13
Genomic location:
Preferred name:
NM_024426.6(WT1):c.500T>A (p.Val167Asp)
HGVS:
  • NC_000011.10:g.32434861A>T
  • NG_009272.1:g.5681T>A
  • NG_050766.2:g.4793A>T
  • NM_000378.6:c.500T>A
  • NM_001407044.1:c.500T>A
  • NM_001407045.1:c.500T>A
  • NM_001407046.1:c.500T>A
  • NM_001407047.1:c.500T>A
  • NM_001407048.1:c.500T>A
  • NM_001407049.1:c.500T>A
  • NM_001407050.1:c.500T>A
  • NM_024424.5:c.500T>A
  • NM_024425.2:c.485T>A
  • NM_024426.6:c.500T>AMANE SELECT
  • NP_000369.4:p.Val167Asp
  • NP_001393973.1:p.Val167Asp
  • NP_001393974.1:p.Val167Asp
  • NP_001393975.1:p.Val167Asp
  • NP_001393976.1:p.Val167Asp
  • NP_001393977.1:p.Val167Asp
  • NP_001393978.1:p.Val167Asp
  • NP_001393979.1:p.Val167Asp
  • NP_077742.3:p.Val167Asp
  • NP_077743.2:p.Val162Asp
  • NP_077744.3:p.Val162Asp
  • NP_077744.4:p.Val167Asp
  • LRG_525t1:c.485T>A
  • LRG_525:g.5681T>A
  • LRG_525p1:p.Val162Asp
  • NC_000011.9:g.32456407A>T
  • NG_050766.1:g.4114A>T
  • NM_024426.3:c.485T>A
  • NR_160306.1:n.679T>A
  • NR_176266.1:n.679T>A
Protein change:
V162D
Links:
dbSNP: rs1853443391
NCBI 1000 Genomes Browser:
rs1853443391
Molecular consequence:
  • NM_000378.6:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407044.1:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407045.1:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407046.1:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407047.1:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407048.1:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407049.1:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407050.1:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024424.5:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024425.2:c.485T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024426.6:c.500T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_160306.1:n.679T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Nephrotic syndrome, type 4 (NPHS4)
Synonyms:
Familial mesangial sclerosis; Nephrotic syndrome, early onset with diffuse mesangial sclerosis
Identifiers:
MONDO: MONDO:0009733; MedGen: C3151568; Orphanet: 656; OMIM: 256370

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001245069Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jan 24, 2020) 		de novoclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not 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 Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV001245069.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

A heterozygous c.485T>A (p.Val162Asp) variant in WT1 was detected in this individual. This variant has not been previously reported or functionally characterized in the literature to our knowledge. It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. The c.485T>A (p.Val162Asp) variant, found in exon 1/10, is predicted by in silico tools to have a deleterious effect on protein function. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. However, low-level parental mosaicism cannot be excluded. Based on the available evidence, the c.485T>A (p.Val162Asp) variant is classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Mar 26, 2023