NM_014625.4(NPHS2):c.124G>A (p.Gly42Arg) AND Nephrotic syndrome, type 2

Germline classification:: Likely benign (2 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:: RCV000665608.2

Allele description [Variation Report for NM_014625.4(NPHS2):c.124G>A (p.Gly42Arg)]

NM_014625.4(NPHS2):c.124G>A (p.Gly42Arg)

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.124G>A (p.Gly42Arg)

HGVS:

NC_000001.11:g.179575741C>T
NG_007535.1:g.5209G>A
NM_001297575.2:c.124G>A
NM_014625.4:c.124G>AMANE SELECT
NP_001284504.1:p.Gly42Arg
NP_055440.1:p.Gly42Arg
NP_055440.1:p.Gly42Arg
LRG_887t1:c.124G>A
LRG_887:g.5209G>A
LRG_887p1:p.Gly42Arg
NC_000001.10:g.179544876C>T
NM_014625.2:c.124G>A
NM_014625.3:c.124G>A

Protein change:

G42R

Links:

dbSNP: rs559836164

NCBI 1000 Genomes Browser:

rs559836164

Molecular consequence:

NM_001297575.2:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_014625.4:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000789758	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely benign (Feb 17, 2017)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17942957, 17699384 Citation Link,
SCV004049302	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

SCV000789758

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely benign
(Feb 17, 2017)

unknown

clinical testing

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

Citation Link,

SCV004049302

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

Citations

PubMed

NPHS2 variation in sporadic focal segmental glomerulosclerosis.

McKenzie LM, Hendrickson SL, Briggs WA, Dart RA, Korbet SM, Mokrzycki MH, Kimmel PL, Ahuja TS, Berns JS, Simon EE, Smith MC, Trachtman H, Michel DM, Schelling JR, Cho M, Zhou YC, Binns-Roemer E, Kirk GD, Kopp JB, Winkler CA.

J Am Soc Nephrol. 2007 Nov;18(11):2987-95. Epub 2007 Oct 17.

PubMed [citation]

PMID:: 17942957
PMCID:: PMC4096868

Recessive NPHS2 (Podocin) mutations are rare in adult-onset idiopathic focal segmental glomerulosclerosis.

He N, Zahirieh A, Mei Y, Lee B, Senthilnathan S, Wong B, Mucha B, Hildebrandt F, Cole DE, Cattran D, Pei Y.

Clin J Am Soc Nephrol. 2007 Jan;2(1):31-7. Epub 2006 Oct 25.

PubMed [citation]

PMID:: 17699384

See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000789758.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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

From Genome-Nilou Lab, SCV004049302.1

#	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: Mar 30, 2024

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