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:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002521567	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 22, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 15253708, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002521567

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 22, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical 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.

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

Last Updated: Mar 30, 2024

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