NM_004646.4(NPHS1):c.1379G>A (p.Arg460Gln) AND Nephrotic syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 10, 2017
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV001849302.2

Allele description [Variation Report for NM_004646.4(NPHS1):c.1379G>A (p.Arg460Gln)]

NM_004646.4(NPHS1):c.1379G>A (p.Arg460Gln)

Gene:

NPHS1:NPHS1 adhesion molecule, nephrin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.12

Genomic location:

Preferred name:

NM_004646.4(NPHS1):c.1379G>A (p.Arg460Gln)

HGVS:

NC_000019.10:g.35848102C>T
NG_013356.2:g.26186G>A
NG_051206.1:g.1468C>T
NM_004646.4:c.1379G>AMANE SELECT
NP_004637.1:p.Arg460Gln
NP_004637.1:p.Arg460Gln
LRG_693t1:c.1379G>A
LRG_693:g.26186G>A
LRG_693p1:p.Arg460Gln
NC_000019.9:g.36339004C>T
NM_004646.3:c.1379G>A
O60500:p.Arg460Gln

Protein change:

R460Q

Links:

UniProtKB: O60500#VAR_064209; dbSNP: rs386833880

Molecular consequence:

NM_004646.4:c.1379G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Nephrotic syndrome
Identifiers:: MONDO: MONDO:0005377; MedGen: C0027726; Human Phenotype Ontology: HP:0000100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002106846	Yale Center for Mendelian Genomics, Yale University - Yale Center for Mendelian Genomics	no assertion criteria provided	Likely pathogenic (Nov 10, 2017)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002106846

Yale Center for Mendelian Genomics, Yale University - Yale Center for Mendelian Genomics

no assertion criteria provided

Likely pathogenic
(Nov 10, 2017)

germline

literature only

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	yes	1	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Whole Exome Sequencing of Patients with Steroid-Resistant Nephrotic Syndrome.

Warejko JK, Tan W, Daga A, Schapiro D, Lawson JA, Shril S, Lovric S, Ashraf S, Rao J, Hermle T, Jobst-Schwan T, Widmeier E, Majmundar AJ, Schneider R, Gee HY, Schmidt JM, Vivante A, van der Ven AT, Ityel H, Chen J, Sadowski CE, Kohl S, et al.

Clin J Am Soc Nephrol. 2018 Jan 6;13(1):53-62. doi: 10.2215/CJN.04120417. Epub 2017 Nov 10.

PubMed [citation]

PMID:: 29127259
PMCID:: PMC5753307

Details of each submission

From Yale Center for Mendelian Genomics, Yale University - Yale Center for Mendelian Genomics, SCV002106846.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	literature only	PubMed (1)

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

Last Updated: Jun 20, 2026

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