NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln) AND Nephrotic syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Dec 20, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001328321.4

Allele description

NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln)

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.413G>A (p.Arg138Gln)

HGVS:

NC_000001.11:g.179561327C>T
NG_007535.1:g.19623G>A
NM_001297575.2:c.413G>A
NM_014625.4:c.413G>AMANE SELECT
NP_001284504.1:p.Arg138Gln
NP_055440.1:p.Arg138Gln
NP_055440.1:p.Arg138Gln
LRG_887t1:c.413G>A
LRG_887:g.19623G>A
LRG_887p1:p.Arg138Gln
NC_000001.10:g.179530462C>T
NM_001297575.2:c.413G>A
NM_014625.2:c.413G>A
NM_014625.3:c.413G>A
Q9NP85:p.Arg138Gln
p.ARG138GLN
p.R138Q

Protein change:

R138Q; ARG138GLN

Links:

UniProtKB: Q9NP85#VAR_010233; OMIM: 604766.0001; dbSNP: rs74315342

NCBI 1000 Genomes Browser:

rs74315342

Molecular consequence:

NM_001297575.2:c.413G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_014625.4:c.413G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV001449390	Sydney Genome Diagnostics, Children's Hospital Westmead	no assertion criteria provided	Pathogenic (Mar 6, 2018)	unknown	clinical testing
SCV002106946	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]
SCV002506421	Institute of Human Genetics, University Hospital Muenster	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 20, 2021)	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

SCV001449390

Sydney Genome Diagnostics, Children's Hospital Westmead

no assertion criteria provided

Pathogenic
(Mar 6, 2018)

unknown

clinical testing

SCV002106946

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]

SCV002506421

Institute of Human Genetics, University Hospital Muenster

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 20, 2021)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing, literature only
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Sydney Genome Diagnostics, Children's Hospital Westmead, SCV001449390.1

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

From Yale Center for Mendelian Genomics, Yale University - Yale Center for Mendelian Genomics, SCV002106946.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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		2	not provided	not provided	not provided

From Institute of Human Genetics, University Hospital Muenster, SCV002506421.1

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

Description

ACMG categories: PS1,PM1,PM2,PP3,PP4,PP5

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

Last Updated: Jun 23, 2024

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