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NM_014625.4(NPHS2):c.352C>T (p.Pro118Ser) AND Nephrotic syndrome, type 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 22, 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:
RCV002251134.1

Allele description [Variation Report for NM_014625.4(NPHS2):c.352C>T (p.Pro118Ser)]

NM_014625.4(NPHS2):c.352C>T (p.Pro118Ser)

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.352C>T (p.Pro118Ser)
HGVS:
  • NC_000001.11:g.179564716G>A
  • NG_007535.1:g.16234C>T
  • NM_001297575.2:c.352C>T
  • NM_014625.4:c.352C>TMANE SELECT
  • NP_001284504.1:p.Pro118Ser
  • NP_055440.1:p.Pro118Ser
  • LRG_887:g.16234C>T
  • NC_000001.10:g.179533851G>A
Protein change:
P118S
Links:
dbSNP: rs2125790124
NCBI 1000 Genomes Browser:
rs2125790124
Molecular consequence:
  • NM_001297575.2:c.352C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014625.4:c.352C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Nephrotic syndrome, type 2 (NPHS2)
Synonyms:
Nephrotic syndrome, steroid-resistant, autosomal recessive; Hereditary nephrotic syndrome
Identifiers:
MONDO: MONDO:0010974; MedGen: C1868672; Orphanet: 656; OMIM: 600995

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV0025215673billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(May 22, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Citations

PubMed

NPHS2 mutation analysis shows genetic heterogeneity of steroid-resistant nephrotic syndrome and low post-transplant recurrence.

Weber S, Gribouval O, Esquivel EL, Morinière V, Tête MJ, Legendre C, Niaudet P, Antignac C.

Kidney Int. 2004 Aug;66(2):571-9.

PubMed [citation]
PMID:
15253708

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 3billion, SCV002521567.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.86; 3Cnet: 0.87). A different missense change at the same codon (p.Pro118Leu) has been reported to be associated with NPHS2 related disorder (ClinVar ID: VCV000222762 / PMID: 15253708). However the evidence of pathogenicity is insufficient at this time. Therefore, this variant is classified as uncertain significanceaccording to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Mar 30, 2024