NM_014625.4(NPHS2):c.288C>T (p.Ser96=) AND Nephrotic syndrome, type 2

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Apr 11, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000576590.7

Allele description [Variation Report for NM_014625.4(NPHS2):c.288C>T (p.Ser96=)]

NM_014625.4(NPHS2):c.288C>T (p.Ser96=)

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.288C>T (p.Ser96=)

HGVS:

NC_000001.11:g.179564780G>A
NG_007535.1:g.16170C>T
NM_001297575.2:c.288C>T
NM_014625.4:c.288C>TMANE SELECT
NP_001284504.1:p.Ser96=
NP_055440.1:p.Ser96=
NP_055440.1:p.Ser96=
LRG_887t1:c.288C>T
LRG_887:g.16170C>T
LRG_887p1:p.Ser96=
NC_000001.10:g.179533915G>A
NM_014625.2:c.288C>T
NM_014625.3:c.288C>T

Links:

dbSNP: rs3738423

NCBI 1000 Genomes Browser:

rs3738423

Molecular consequence:

NM_001297575.2:c.288C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_014625.4:c.288C>T - synonymous variant - [Sequence Ontology: SO:0001819]

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

Recent activity

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Homo sapiens translocase of inner mitochondrial membrane 17A (TIMM17A), mRNA
Homo sapiens translocase of inner mitochondrial membrane 17A (TIMM17A), mRNA
gi|208610007|ref|NM_006335.2|

Nucleotide
Homo sapiens sushi domain containing 4, mRNA (cDNA clone MGC:11193 IMAGE:3926397...
Homo sapiens sushi domain containing 4, mRNA (cDNA clone MGC:11193 IMAGE:3926397), complete cds
gi|33871233|gb|BC004888.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000351505	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Mar 6, 2018)	germline	clinical testing	Citation Link,
SCV000677371	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Apr 29, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11805166, 12707396, 26467025
SCV004049292	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 11, 2023)	germline	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

SCV000351505

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Mar 6, 2018)

germline

clinical testing

Citation Link,

SCV000677371

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Apr 29, 2017)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004049292

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Apr 11, 2023)

germline

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	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel mutations in NPHS2 detected in both familial and sporadic steroid-resistant nephrotic syndrome.

Karle SM, Uetz B, Ronner V, Glaeser L, Hildebrandt F, Fuchshuber A.

J Am Soc Nephrol. 2002 Feb;13(2):388-393. doi: 10.1681/ASN.V132388.

PubMed [citation]

PMID:: 11805166

Broadening the spectrum of diseases related to podocin mutations.

Caridi G, Bertelli R, Di Duca M, Dagnino M, Emma F, Onetti Muda A, Scolari F, Miglietti N, Mazzucco G, Murer L, Carrea A, Massella L, Rizzoni G, Perfumo F, Ghiggeri GM.

J Am Soc Nephrol. 2003 May;14(5):1278-86.

PubMed [citation]

PMID:: 12707396

See all PubMed Citations (4)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000351505.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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

From Athena Diagnostics, SCV000677371.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

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

From Genome-Nilou Lab, SCV004049292.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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