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NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln) AND Nephrotic syndrome

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Dec 20, 2021
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:
RCV001328321.4

Allele description [Variation Report for NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln)]

NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln)

Gene:
NPHS2:NPHS2 stomatin family member, podocin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q25.2
Genomic location:
Preferred name:
NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln)
HGVS:
  • NC_000001.11:g.179561327C>T
  • NG_007535.1:g.19623G>A
  • NM_001297575.2:c.413G>A
  • NM_014625.4:c.413G>AMANE SELECT
  • NP_001284504.1:p.Arg138Gln
  • NP_055440.1:p.Arg138Gln
  • NP_055440.1:p.Arg138Gln
  • LRG_887t1:c.413G>A
  • LRG_887:g.19623G>A
  • LRG_887p1:p.Arg138Gln
  • NC_000001.10:g.179530462C>T
  • NM_001297575.2:c.413G>A
  • NM_014625.2:c.413G>A
  • NM_014625.3:c.413G>A
  • Q9NP85:p.Arg138Gln
  • p.ARG138GLN
  • p.R138Q
Protein change:
R138Q; ARG138GLN
Links:
UniProtKB: Q9NP85#VAR_010233; OMIM: 604766.0001; dbSNP: rs74315342
NCBI 1000 Genomes Browser:
rs74315342
Molecular consequence:
  • NM_001297575.2:c.413G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014625.4:c.413G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Name:
Nephrotic syndrome
Identifiers:
MONDO: MONDO:0005377; MedGen: C0027726; Human Phenotype Ontology: HP:0000100

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001449390Sydney Genome Diagnostics, Children's Hospital Westmead
no assertion criteria provided
Pathogenic
(Mar 6, 2018)
unknownclinical testing

SCV002106946Yale Center for Mendelian Genomics, Yale University - Yale Center for Mendelian Genomics
no assertion criteria provided
Likely pathogenic
(Nov 10, 2017)
germlineliterature only

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

SCV002506421Institute of Human Genetics, University Hospital Muenster
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 20, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing, literature only
not providedunknownyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Whole Exome Sequencing of Patients with Steroid-Resistant Nephrotic Syndrome.

Warejko JK, Tan W, Daga A, Schapiro D, Lawson JA, Shril S, Lovric S, Ashraf S, Rao J, Hermle T, Jobst-Schwan T, Widmeier E, Majmundar AJ, Schneider R, Gee HY, Schmidt JM, Vivante A, van der Ven AT, Ityel H, Chen J, Sadowski CE, Kohl S, et al.

Clin J Am Soc Nephrol. 2018 Jan 6;13(1):53-62. doi: 10.2215/CJN.04120417. Epub 2017 Nov 10.

PubMed [citation]
PMID:
29127259
PMCID:
PMC5753307

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 Sydney Genome Diagnostics, Children's Hospital Westmead, SCV001449390.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

From Yale Center for Mendelian Genomics, Yale University - Yale Center for Mendelian Genomics, SCV002106946.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From Institute of Human Genetics, University Hospital Muenster, SCV002506421.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

ACMG categories: PS1,PM1,PM2,PP3,PP4,PP5

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providedbloodnot provided1not providednot providednot provided

Last Updated: May 19, 2024