NM_014625.4(NPHS2):c.695C>T (p.Thr232Ile) AND Nephrotic syndrome, type 2

Germline classification:: Uncertain significance (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:: RCV000671929.3

Allele description [Variation Report for NM_014625.4(NPHS2):c.695C>T (p.Thr232Ile)]

NM_014625.4(NPHS2):c.695C>T (p.Thr232Ile)

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.695C>T (p.Thr232Ile)

HGVS:

NC_000001.11:g.179557070G>A
NG_007535.1:g.23880C>T
NM_001297575.2:c.535-2539C>T
NM_014625.4:c.695C>TMANE SELECT
NP_055440.1:p.Thr232Ile
LRG_887:g.23880C>T
NC_000001.10:g.179526205G>A
NM_014625.2:c.695C>T

Protein change:

T232I

Links:

dbSNP: rs774199987

NCBI 1000 Genomes Browser:

rs774199987

Molecular consequence:

NM_001297575.2:c.535-2539C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_014625.4:c.695C>T - 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
SCV000796966	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Jan 5, 2018)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24511133, 18823551 Citation Link,
SCV002801321	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 5, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004049268	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]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000796966

Counsyl

criteria provided, single submitter

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

Uncertain significance
(Jan 5, 2018)

unknown

clinical testing

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

Citation Link,

SCV002801321

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 5, 2022)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004049268

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]

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

Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.

Rinschen MM, Wu X, König T, Pisitkun T, Hagmann H, Pahmeyer C, Lamkemeyer T, Kohli P, Schnell N, Schermer B, Dryer S, Brooks BR, Beltrao P, Krueger M, Brinkkoetter PT, Benzing T.

J Am Soc Nephrol. 2014 Jul;25(7):1509-22. doi: 10.1681/ASN.2013070760. Epub 2014 Feb 7.

PubMed [citation]

PMID:: 24511133
PMCID:: PMC4073431

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

See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000796966.1

#	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 Fulgent Genetics, Fulgent Genetics, SCV002801321.1

#	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, SCV004049268.1

#	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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