NPHS2 NPHS2 stomatin family member, podocin [Homo sapiens (human)] - Gene

Summary

Official Symbol: NPHS2provided by HGNC
Official Full Name: NPHS2 stomatin family member, podocinprovided by HGNC
Primary source: HGNC:HGNC:13394
See related: Ensembl:ENSG00000116218 MIM:604766; AllianceGenome:HGNC:13394
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PDCN; SRN1
Summary: This gene encodes a protein that plays a role in the regulation of glomerular permeability. Mutations in this gene cause steroid-resistant nephrotic syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression: Restricted expression toward kidney (RPKM 45.3) See more
Orthologs: mouse all
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Genomic context

Location:: 1q25.2

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (179550539..179575948, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (178905541..178930958, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (179519674..179545083, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A small molecule chaperone rescues keratin-8 mediated trafficking of misfolded podocin to correct genetic Nephrotic Syndrome.
Title: A small molecule chaperone rescues keratin-8 mediated trafficking of misfolded podocin to correct genetic Nephrotic Syndrome.
Copy number variation analysis in 138 families with steroid-resistant nephrotic syndrome identifies causal homozygous deletions in PLCE1 and NPHS2 in two families.
Title: Copy number variation analysis in 138 families with steroid-resistant nephrotic syndrome identifies causal homozygous deletions in PLCE1 and NPHS2 in two families.
Analysis of the association of NPHS2 and ACTN4 genes polymorphism with nephrotic syndrome in Egyptian children.
Title: Analysis of the association of NPHS2 and ACTN4 genes polymorphism with nephrotic syndrome in Egyptian children.
Kidney Organoids Generated Using an Allelic Series of NPHS2 Point Variants Reveal Distinct Intracellular Podocin Mistrafficking.
Title: Kidney Organoids Generated Using an Allelic Series of NPHS2 Point Variants Reveal Distinct Intracellular Podocin Mistrafficking.
Spectrum of NPHS1 and NPHS2 variants in egyptian children with focal segmental glomerular sclerosis: identification of six novel variants and founder effect.
Title: Spectrum of NPHS1 and NPHS2 variants in egyptian children with focal segmental glomerular sclerosis: identification of six novel variants and founder effect.
A novel NPHS2 mutation (c.865A > G) identified in a Chinese family with steroid-resistant nephrotic syndrome alters subcellular localization of nephrin.
Title: A novel NPHS2 mutation (c.865A > G) identified in a Chinese family with steroid-resistant nephrotic syndrome alters subcellular localization of nephrin.
NPHS2 gene polymorphism aggravates renal damage caused by focal segmental glomerulosclerosis with COL4A3 mutation.
Title: NPHS2 gene polymorphism aggravates renal damage caused by focal segmental glomerulosclerosis with COL4A3 mutation.
A Study of the Risk Factors and Urinary Podocin as an Early Prognostic Indicator of Renal Injury in Diabetic Nephropathy.
Title: A Study of the Risk Factors and Urinary Podocin as an Early Prognostic Indicator of Renal Injury in Diabetic Nephropathy.
Generation of an induced pluripotent stem cell (iPSC) line (IMAGINi007) from a patient with steroid-resistant nephrotic syndrome carrying the homozygous p.R138Q mutation in the podocin-encoding NPHS2 gene.
Title: Generation of an induced pluripotent stem cell (iPSC) line (IMAGINi007) from a patient with steroid-resistant nephrotic syndrome carrying the homozygous p.R138Q mutation in the podocin-encoding NPHS2 gene.
Analysis of the clinical characteristics of arthritis with renal disease caused by a NPHS2 gene mutation.
Title: Analysis of the clinical characteristics of arthritis with renal disease caused by a NPHS2 gene mutation.

Submit: New GeneRIF Correction See all GeneRIFs (134)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Nephrotic syndrome, type 2 MedGen: C1868672 OMIM: 600995 GeneReviews: Genetic Steroid-Resistant Nephrotic Syndrome Overview	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NPHS2__6070 (e-PCR)
- UniSTS:463643

PMC151634P1 (e-PCR)
- UniSTS:271156

PMC151634P2 (e-PCR)
- UniSTS:271157

RH92018 (e-PCR)
- UniSTS:88117

PMC151634P3 (e-PCR)
- UniSTS:271158

PMC151634P4 (e-PCR)
- UniSTS:271159

PMC151634P5 (e-PCR)
- UniSTS:271160

D1S1640 (e-PCR)
- UniSTS:16039

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	IDA Inferred from Direct Assay more info	PubMed
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in glomerular filtration	TAS Traceable Author Statement more info	PubMed
involved_in metanephric podocyte development	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in cell-cell junction	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in membrane raft	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with slit diaphragm	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: podocin

Names: NPHS2, podocin; nephrosis 2, idiopathic, steroid-resistant (podocin)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007535.1 RefSeqGene

Range

4998..30411

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_887

mRNA and Protein(s)

NM_001297575.2 → NP_001284504.1 podocin isoform 2

See identical proteins and their annotated locations for NP_001284504.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AL160286, BC029141, BI831348, BX095913

Consensus CDS

CCDS72988.1

UniProtKB/Swiss-Prot

Q9NP85

Related

ENSP00000356588.4, ENST00000367616.4

Conserved Domains (1) summary

cl19107
Location:122 → 276

SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
NM_014625.4 → NP_055440.1 podocin isoform 1

See identical proteins and their annotated locations for NP_055440.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AJ279254, AL160286, BC029141, BX095913

Consensus CDS

CCDS1331.1

UniProtKB/Swiss-Prot

B1AM32, B1AM33, Q8N6Q5, Q9NP85

Related

ENSP00000356587.4, ENST00000367615.9

Conserved Domains (2) summary

smart00244
Location:123 → 287

PHB; prohibitin homologues

cd08827
Location:122 → 344

SPFH_podocin; Podocin, a subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

179550539..179575948 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005245483.4 → XP_005245540.1 podocin isoform X1

Conserved Domains (2) summary

smart00244
Location:90 → 228

PHB; prohibitin homologues

cl19107
Location:92 → 285

SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
XM_017002298.2 → XP_016857787.1 podocin isoform X2
XM_017002299.2 → XP_016857788.1 podocin isoform X3