NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln) AND Chronic kidney disease

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 28, 2020
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:: RCV001171338.2

Allele description [Variation Report for NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln)]

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]

Condition(s)

Name:: Chronic kidney disease
Identifiers:: MONDO: MONDO:0005300; MedGen: C1561643; Human Phenotype Ontology: HP:0012622

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001328285	Cavalleri Lab, Royal College of Surgeons in Ireland	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 28, 2020)	unknown	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001328285

Cavalleri Lab, Royal College of Surgeons in Ireland

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(May 28, 2020)

unknown

research

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	yes	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

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 Cavalleri Lab, Royal College of Surgeons in Ireland, SCV001328285.1

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

Description

PS3, PP3, PP5

#	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		not provided	not provided	not provided	not provided

Last Updated: Apr 20, 2025

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