NPHS1 NPHS1 adhesion molecule, nephrin [Homo sapiens (human)] - Gene

Summary

Official Symbol: NPHS1provided by HGNC
Official Full Name: NPHS1 adhesion molecule, nephrinprovided by HGNC
Primary source: HGNC:HGNC:7908
See related: Ensembl:ENSG00000161270 MIM:602716; AllianceGenome:HGNC:7908
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: CNF; NPHN; nephrin
Summary: This gene encodes a member of the immunoglobulin family of cell adhesion molecules that functions in the glomerular filtration barrier in the kidney. The gene is primarily expressed in renal tissues, and the protein is a type-1 transmembrane protein found at the slit diaphragm of glomerular podocytes. The slit diaphragm is thought to function as an ultrafilter to exclude albumin and other plasma macromolecules in the formation of urine. Mutations in this gene result in Finnish-type congenital nephrosis 1, characterized by severe proteinuria and loss of the slit diaphragm and foot processes.[provided by RefSeq, Oct 2009]
Expression: Biased expression in kidney (RPKM 12.8), pancreas (RPKM 3.0) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.12

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (35825372..35852504, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (38370677..38398258, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (36316274..36343406, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Anti-nephrin antibodies in steroid-sensitive nephrotic syndrome in Japanese children.
Title: Anti-nephrin antibodies in steroid-sensitive nephrotic syndrome in Japanese children.
Loss of S1P Lyase Expression in Human Podocytes Causes a Reduction in Nephrin Expression That Involves PKCdelta Activation.
Title: Loss of S1P Lyase Expression in Human Podocytes Causes a Reduction in Nephrin Expression That Involves PKCδ Activation.
Clinicopathological Impact of Gene Polymorphism of Nephrin and Glucocorticoid Receptor Genes in Egyptian Children with Nonfamilial Nephrotic Syndrome.
Title: Clinicopathological Impact of Gene Polymorphism of Nephrin and Glucocorticoid Receptor Genes in Egyptian Children with Nonfamilial Nephrotic Syndrome.
Nephrin expression in human epidermal keratinocytes and its implication in poor wound closure.
Title: Nephrin expression in human epidermal keratinocytes and its implication in poor wound closure.
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.
Urinary Matrix Metalloproteinase-9 and Nephrin in Idiopathic Membranous Nephropathy: A Cross-Sectional Study.
Title: Urinary Matrix Metalloproteinase-9 and Nephrin in Idiopathic Membranous Nephropathy: A Cross-Sectional Study.
The association of NPHS1 and ACNT4 gene polymorphisms with pre-eclampsia.
Title: The association of NPHS1 and ACNT4 gene polymorphisms with pre-eclampsia.
Endoplasmic reticulum-associated degradation is required for nephrin maturation and kidney glomerular filtration function.
Title: Endoplasmic reticulum-associated degradation is required for nephrin maturation and kidney glomerular filtration function.
Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome.
Title: Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome.
[Analysis of a sib-pair with Finnish type congenital nephrotic syndrome due to variant of NPHS1 gene].
Title: [Analysis of a sib-pair with Finnish type congenital nephrotic syndrome due to variant of NPHS1 gene].

Submit: New GeneRIF Correction See all GeneRIFs (128)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Finnish congenital nephrotic syndrome MedGen: C0403399 OMIM: 256300 GeneReviews: Genetic Steroid-Resistant Nephrotic Syndrome Overview	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat rapidly induces the redistribution and loss of nephrin by engaging vascular endothelial growth factor receptors types 2 and 3 and the integrin alphavbeta3 in cultured human podocytes	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NPHS1__6069 (e-PCR)
- UniSTS:463642

PMC156606P1 (e-PCR)
- UniSTS:271408

D1S1423 (e-PCR)
- UniSTS:149619

PMC164293P1 (e-PCR)
- UniSTS:271482

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	IBA Inferred from Biological aspect of Ancestor more info
enables myosin binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in JNK cascade	IEA Inferred from Electronic Annotation more info
involved_in cell-cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in glomerular basement membrane development	IEP Inferred from Expression Pattern more info	PubMed
involved_in myoblast fusion	IEA Inferred from Electronic Annotation more info
involved_in podocyte development	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of actin filament polymerization	IEA Inferred from Electronic Annotation more info
involved_in protein localization to synapse	IGI Inferred from Genetic Interaction more info	PubMed
involved_in skeletal muscle tissue development	IEA Inferred from Electronic Annotation more info
involved_in slit diaphragm assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in slit diaphragm assembly	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in cell-cell junction	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular exosome	HDA more info	PubMed
located_in focal adhesion	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in slit diaphragm	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: nephrin

Names: NPHS1, nephrin; nephrosis 1, congenital, Finnish type (nephrin); renal glomerulus-specific cell adhesion receptor

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_013356.2 RefSeqGene

Range

22295..48916

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_693

mRNA and Protein(s)

NM_004646.4 → NP_004637.1 nephrin precursor

See identical proteins and their annotated locations for NP_004637.1

Status: REVIEWED

Source sequence(s)

AC002133, U95090

Consensus CDS

CCDS32996.1

UniProtKB/Swiss-Prot

A6NDH2, C3RX61, O60500

Related

ENSP00000368190.4, ENST00000378910.10

Conserved Domains (8) summary

cd05773
Location:834 → 942

Ig8_hNephrin_like; Eighth immunoglobulin-like domain of nephrin

smart00410
Location:845 → 935

IG_like; Immunoglobulin like

pfam07679
Location:646 → 736

I-set; Immunoglobulin I-set domain

pfam00041
Location:942 → 1023

fn3; Fibronectin type III domain

pfam07686
Location:38 → 119

V-set; Immunoglobulin V-set domain

pfam08205
Location:141 → 228

C2-set_2; CD80-like C2-set immunoglobulin domain

pfam13927
Location:739 → 820

Ig_3; Immunoglobulin domain

cl11960
Location:345 → 424

Ig; Immunoglobulin domain