NM_014625.4(NPHS2):c.671G>A (p.Arg224His) AND Nephrotic syndrome, type 2

Germline classification:: Uncertain significance (4 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:: RCV000671743.7

Allele description [Variation Report for NM_014625.4(NPHS2):c.671G>A (p.Arg224His)]

NM_014625.4(NPHS2):c.671G>A (p.Arg224His)

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.671G>A (p.Arg224His)

HGVS:

NC_000001.11:g.179557094C>T
NG_007535.1:g.23856G>A
NM_001297575.2:c.535-2563G>A
NM_014625.4:c.671G>AMANE SELECT
NP_055440.1:p.Arg224His
LRG_887:g.23856G>A
NC_000001.10:g.179526229C>T
NM_014625.2:c.671G>A

Protein change:

R224H

Links:

dbSNP: rs138545216

NCBI 1000 Genomes Browser:

rs138545216

Molecular consequence:

NM_001297575.2:c.535-2563G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_014625.4:c.671G>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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truncated aldo-keto reductase [Homo sapiens]
truncated aldo-keto reductase [Homo sapiens]
gi|7328952|dbj|BAA92887.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000796756	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Dec 28, 2017)	unknown	clinical testing	Citation Link,
SCV001258327	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 29, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 18823551, 18726620 Citation Link,
SCV002784293	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 8, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004049270	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 11, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
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 focal and segmental glomerulosclerosis.

Tonna SJ, Needham A, Polu K, Uscinski A, Appel GB, Falk RJ, Katz A, Al-Waheeb S, Kaplan BS, Jerums G, Savige J, Harmon J, Zhang K, Curhan GC, Pollak MR.

BMC Nephrol. 2008 Sep 29;9:13. doi: 10.1186/1471-2369-9-13.

PubMed [citation]

PMID:: 18823551
PMCID:: PMC2569023

The R229Q mutation in NPHS2 may predispose to proteinuria in thin-basement-membrane nephropathy.

Tonna S, Wang YY, Wilson D, Rigby L, Tabone T, Cotton R, Savige J.

Pediatr Nephrol. 2008 Dec;23(12):2201-7. doi: 10.1007/s00467-008-0934-7. Epub 2008 Aug 26.

PubMed [citation]

PMID:: 18726620

See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000796756.1

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

#	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 Illumina Laboratory Services, Illumina, SCV001258327.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	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 Fulgent Genetics, Fulgent Genetics, SCV002784293.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV004049270.1

#	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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