NM_024426.6(WT1):c.1504G>C (p.Asp502His) AND Nephrotic syndrome, type 4

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 1, 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:: RCV004577627.1

Allele description [Variation Report for NM_024426.6(WT1):c.1504G>C (p.Asp502His)]

NM_024426.6(WT1):c.1504G>C (p.Asp502His)

Gene:

WT1:WT1 transcription factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_024426.6(WT1):c.1504G>C (p.Asp502His)

HGVS:

NC_000011.10:g.32389123C>G
NG_009272.1:g.51419G>C
NM_000378.6:c.1444G>C
NM_001198551.2:c.844G>C
NM_001198552.2:c.802G>C
NM_001367854.1:c.316G>C
NM_001407044.1:c.1489G>C
NM_001407045.1:c.1453G>C
NM_001407046.1:c.1411G>C
NM_001407047.1:c.1372G>C
NM_001407048.1:c.1363G>C
NM_001407049.1:c.1360G>C
NM_001407050.1:c.1330G>C
NM_001407051.1:c.742G>C
NM_024424.5:c.1495G>C
NM_024425.2:c.1438G>C
NM_024426.6:c.1504G>CMANE SELECT
NP_000369.4:p.Asp482His
NP_001185480.1:p.Asp282His
NP_001185480.1:p.Asp282His
NP_001185481.1:p.Asp268His
NP_001354783.1:p.Asp106His
NP_001393973.1:p.Asp497His
NP_001393974.1:p.Asp485His
NP_001393975.1:p.Asp471His
NP_001393976.1:p.Asp458His
NP_001393977.1:p.Asp455His
NP_001393978.1:p.Asp454His
NP_001393979.1:p.Asp444His
NP_001393980.1:p.Asp248His
NP_077742.3:p.Asp499His
NP_077743.2:p.Asp480His
NP_077744.3:p.Asp497His
NP_077744.4:p.Asp502His
LRG_525t1:c.1489G>C
LRG_525t2:c.844G>C
LRG_525:g.51419G>C
LRG_525p1:p.Asp497His
LRG_525p2:p.Asp282His
NC_000011.9:g.32410669C>G
NM_001198551.1:c.844G>C
NM_024426.3:c.1489G>C
NR_160306.1:n.1836G>C
NR_176266.1:n.1776G>C

Protein change:

D106H

Molecular consequence:

NM_000378.6:c.1444G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001198551.2:c.844G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001198552.2:c.802G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001367854.1:c.316G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407044.1:c.1489G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407045.1:c.1453G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407046.1:c.1411G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407047.1:c.1372G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407048.1:c.1363G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407049.1:c.1360G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407050.1:c.1330G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407051.1:c.742G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024424.5:c.1495G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024425.2:c.1438G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024426.6:c.1504G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_160306.1:n.1836G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176266.1:n.1776G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Recent activity

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gi|74226127|dbj|AK143124.1|

Nucleotide
Uncultured Tuber clone Q-L-OTU333 18S ribosomal RNA gene, partial sequence; inte...
Uncultured Tuber clone Q-L-OTU333 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
gi|1315691602|gb|KY684691.1|

Nucleotide
Californiconus californicus isolate BC_5 NADH dehydrogenase subunit 2 (ND2) gene...
Californiconus californicus isolate BC_5 NADH dehydrogenase subunit 2 (ND2) gene, partial cds; mitochondrial
gi|339655447|gb|HQ728043.1|

Nucleotide
Californiconus californicus isolate BC_3 NADH dehydrogenase subunit 2 (ND2) gene...
Californiconus californicus isolate BC_3 NADH dehydrogenase subunit 2 (ND2) gene, partial cds; mitochondrial
gi|339655451|gb|HQ728045.1|

Nucleotide
Chain A, Polyubiquitin-C
Chain A, Polyubiquitin-C
gi|449802157|pdb|3VUY|A

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004218505	Precision Medicine Center, Zhengzhou University	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 1, 2023)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004218505

Precision Medicine Center, Zhengzhou University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Dec 1, 2023)

de novo

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical 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 Precision Medicine Center, Zhengzhou University, SCV004218505.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

PS2,PM2_p,PP3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 29, 2024

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