Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	7827
Gene name Gene Name - the full gene name approved by the HGNC.	NPHS2 stomatin family member, podocin
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	NPHS2
Synonyms (NCBI Gene) Gene synonyms aliases	PDCN, SRN1
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q25.2
Summary Summary of gene provided in NCBI Entrez Gene.	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]

Show/Hide all(46)

SNP ID	Visualize variation	Clinical significance	Consequence
rs12406197	C>A	Pathogenic, likely-pathogenic, likely-benign	5 prime UTR variant
rs12568913	G>A,C,T	Likely-pathogenic	Stop gained, coding sequence variant, intron variant, synonymous variant, missense variant
rs61747728	C>T	Uncertain-significance, pathogenic, likely-pathogenic, risk-factor	Missense variant, coding sequence variant, intron variant
rs74315342	C>T	Conflicting-interpretations-of-pathogenicity, pathogenic	Missense variant, coding sequence variant, intron variant
rs74315343	G>A	Pathogenic	Stop gained, coding sequence variant, intron variant
rs74315344	G>A	Pathogenic, benign-likely-benign	Missense variant, coding sequence variant
rs74315345	C>A,G,T	Pathogenic	Missense variant, coding sequence variant
rs74315346	T>A,C	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs74315347	C>T	Pathogenic	Missense variant, coding sequence variant, intron variant
rs78541594	G>C	Likely-benign, pathogenic	5 prime UTR variant
rs528833893	A>-,AA	Pathogenic, conflicting-interpretations-of-pathogenicity	Coding sequence variant, frameshift variant
rs530318579	C>T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs748812981	C>A	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant, intron variant
rs755972674	G>A	Pathogenic	Intron variant, coding sequence variant, stop gained
rs762631237	C>A,T	Pathogenic	Intron variant, splice donor variant
rs778055996	G>A,C	Likely-pathogenic, pathogenic	Intron variant, stop gained, missense variant, coding sequence variant
rs786204583	G>A	Likely-pathogenic	Missense variant, coding sequence variant, synonymous variant
rs786204708	A>T	Pathogenic, likely-pathogenic	Splice donor variant, intron variant
rs869025495	G>A	Pathogenic	Missense variant, coding sequence variant, intron variant
rs869312746	G>A	Pathogenic	Coding sequence variant, stop gained
rs878853211	T>A	Drug-response	Intron variant
rs878853212	G>A	Drug-response	Intron variant
rs878853213	A>C	Drug-response	Intron variant
rs878853214	A>C	Drug-response	Intron variant
rs878853215	C>A,T	Drug-response	Missense variant, coding sequence variant
rs878853216	C>T	Drug-response	5 prime UTR variant
rs1057516395	G>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1057516414	G>A,T	Likely-pathogenic	Stop gained, intron variant, coding sequence variant, synonymous variant
rs1057516680	C>A,T	Likely-pathogenic	Initiator codon variant, missense variant
rs1057516747	->AGCCC	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057516880	->TA	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1060499703	C>T	Pathogenic	Splice acceptor variant
rs1167223941	C>A,T	Likely-pathogenic	Stop gained, missense variant, coding sequence variant
rs1212702104	A>G	Likely-pathogenic	Splice donor variant, intron variant
rs1272948499	C>-	Pathogenic-likely-pathogenic	Frameshift variant, coding sequence variant
rs1291398331	C>A	Pathogenic	Intron variant, splice acceptor variant
rs1320543506	->C	Pathogenic	Frameshift variant, coding sequence variant
rs1462028977	G>A	Pathogenic	Stop gained, coding sequence variant
rs1553315173	T>C	Likely-pathogenic	Splice acceptor variant, intron variant
rs1553316575	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1553316611	->C	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1553316648	T>CC	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1553316670	->T	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1558355124	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1572277600	AA>-	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1572282458	C>T	Likely-pathogenic	Coding sequence variant, intron variant, missense variant

Show/Hide all(25)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018421	hsa-miR-335-5p	Microarray	18185580
MIRT735673	hsa-miR-185-5p	Luciferase reporter assay, Western blotting, Immunohistochemistry (IHC), qRT-PCR	33977784
MIRT735673	hsa-miR-185-5p	Luciferase reporter assay, Western blotting, Microarray, Immunoprecipitaion (IP), Immunohistochemistry (IHC), qRT-PCR	33977784
MIRT1190901	hsa-miR-1294	CLIP-seq
MIRT1190902	hsa-miR-134	CLIP-seq
MIRT1190903	hsa-miR-183	CLIP-seq
MIRT1190904	hsa-miR-3118	CLIP-seq
MIRT1190905	hsa-miR-3127-5p	CLIP-seq
MIRT1190906	hsa-miR-3164	CLIP-seq
MIRT1190907	hsa-miR-3607-5p	CLIP-seq
MIRT1190908	hsa-miR-3915	CLIP-seq
MIRT1190909	hsa-miR-3928	CLIP-seq
MIRT1190910	hsa-miR-4269	CLIP-seq
MIRT1190911	hsa-miR-4316	CLIP-seq
MIRT1190912	hsa-miR-4501	CLIP-seq
MIRT1190913	hsa-miR-4514	CLIP-seq
MIRT1190914	hsa-miR-4692	CLIP-seq
MIRT1190915	hsa-miR-4742-5p	CLIP-seq
MIRT2055242	hsa-miR-129-5p	CLIP-seq
MIRT2055243	hsa-miR-33a	CLIP-seq
MIRT2055244	hsa-miR-33b	CLIP-seq
MIRT2055245	hsa-miR-450b-5p	CLIP-seq
MIRT2055246	hsa-miR-4639-3p	CLIP-seq
MIRT2055247	hsa-miR-507	CLIP-seq
MIRT2055248	hsa-miR-557	CLIP-seq

Transcription factors

Show/Hide all(2)

Transcription factor	Regulation	Reference
LMX1B	Unknown	11956244;11956245
USF1	Unknown	16572591

Show/Hide all(20)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003094	Process	Glomerular filtration	TAS	10742096
GO:0005515	Function	Protein binding	IPI	12424224, 17675666, 22662192
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	10742096
GO:0005911	Component	Cell-cell junction	IDA	17675666
GO:0009898	Component	Cytoplasmic side of plasma membrane	IDA	11786407
GO:0009898	Component	Cytoplasmic side of plasma membrane	IEA
GO:0010467	Process	Gene expression	IEA
GO:0016020	Component	Membrane	IEA
GO:0030036	Process	Actin cytoskeleton organization	IDA	17675666
GO:0032991	Component	Protein-containing complex	IDA	17675666
GO:0036057	Component	Slit diaphragm	IDA	11786407
GO:0036057	Component	Slit diaphragm	IEA
GO:0045121	Component	Membrane raft	IDA	17675666
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145
GO:0071944	Component	Cell periphery	IEA
GO:0072001	Process	Renal system development	IBA
GO:0072249	Process	Metanephric podocyte development	IEP	11786407

MIM	HGNC	e!Ensembl
604766	13394	ENSG00000116218

Protein

UniProt ID

Q9NP85

Protein name

Podocin

Protein function

Plays a role in the regulation of glomerular permeability, acting probably as a linker between the plasma membrane and the cytoskeleton.

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01145	Band_7	126 → 300	SPFH domain / Band 7 family	Family

Tissue specificity

TISSUE SPECIFICITY: Almost exclusively expressed in the podocytes of fetal and mature kidney glomeruli.

Sequence

MERRARSSSRESRGRGGRTPHKENKRAKAERSGGGRGRQEAGPEPSGSGRAGTPGEPRAP
AATVVDVDEVRGSGEEGTEVVALLESERPEEGTKSSGLGACEWLLVLISLLFIIMTFPFS
IWFCVKVVQEYERVIIFRLGHLLPGRAKGPGLFFFLPCLDTYHKVDLRLQTLEIPFHEIV
TKDMFIMEIDAICYYRMENASLLLSSLAHVSKAVQFLVQTTMKRLLAHRSLTEILLERKS
IAQDAKVALDSVTCIWGIKVERIEIKDVRLPAGLQHSLAVEAEAQRQAKVRMIAAEAEKA
ASESLRMAAEILSGTPAAVQLRYLHTLQSLSTEKPSTVVLPLPFDLLNCLSSPSNRTQGS
LPFPSPSKPVEPLNPKKKDSPML

Sequence length

383

Interactions

View interactions

	Reactome
			Nephrin family interactions

Show/Hide Causal Diseases (6)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Finnish Congenital Nephrotic Syndrome	finnish congenital nephrotic syndrome	rs530318579	N/A
focal segmental glomerulosclerosis	Focal segmental glomerulosclerosis	rs74315343, rs748812981	N/A
Nephrotic Syndrome	Nephrotic syndrome, type 2, nephrotic syndrome	rs748812981, rs530318579, rs199506378, rs1553316648, rs1060499703, rs1553316611, rs775006954, rs74315345, rs755972674, rs1057517164, rs780761368, rs74315346, rs1553312833, rs1057516523, rs1558355124 View all (35 more)	N/A
proteinuria	Proteinuria	rs869025495	N/A
Steroid resistant nephrotic syndrome	Steroid-resistant nephrotic syndrome	rs530318579, rs775006954, rs74315347, rs778055996, rs74315342, rs1291398331, rs74315348, rs775170915, rs748812981, rs74315343	N/A
Kidney Disease	Chronic kidney disease	rs74315342	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Gout	Gout	N/A	N/A	GWAS

Show/Hide Text Mining Associations (37)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Albuminuria	Associate	18499321, 18823551, 24103534
Anti Glomerular Basement Membrane Disease	Associate	14633131
Carcinoma Renal Cell	Associate	26831905
Chromosome Aberrations	Associate	14871423
Cicatrix	Associate	20370455
Diabetes Mellitus	Associate	18823551
Diabetic Nephropathies	Associate	17264876, 21655212
Diabetic Nephropathies	Inhibit	22615747
Disease	Associate	12368218, 29637272
Edema	Associate	32779421
Fibrosis	Associate	17264876
Genetic Diseases Inborn	Associate	24509478, 28780565
Glomerulonephritis IGA	Associate	14633131, 22578956, 23982418
Glomerulonephritis Membranoproliferative	Associate	23982418
Glomerulosclerosis Focal Segmental	Associate	12464671, 14633131, 15015071, 15253708, 17109732, 17942957, 18499321, 18823551, 20947785, 21355056, 23982418, 24089165, 24856380, 25112471, 28629718 View all (9 more)
Glomerulosclerosis Focal Segmental	Inhibit	28629718
Hypoalbuminemia	Associate	32779421
Ichthyosis X Linked	Associate	35920919
Kidney Diseases	Associate	14633131, 15149332, 16572591, 18499321, 22119407, 23982418, 24157943, 25112471, 26420286, 30691124, 32585588, 33305316
Kidney Failure Chronic	Associate	15954915, 16050398, 16572591, 19145239, 20947785, 24089165, 24157943, 27193387
Kidney Neoplasms	Associate	31754646, 37510393
Neoplastic Syndromes Hereditary	Associate	23645318, 31922211
Nephrosis	Associate	18823551
Nephrosis congenital	Associate	12368218, 15338398, 15780077, 16050398, 18614772, 19406966, 22578956, 24509478, 25635037, 25729976, 26668027, 30514835
Nephrosis Lipoid	Associate	14633131
Nephrotic Syndrome	Associate	11786407, 14633131, 14871423, 15015071, 15253708, 15327385, 15338398, 15496146, 15954915, 16050398, 16572591, 17109732, 18216321, 18499321, 18543005 View all (40 more)
Nephrotic syndrome idiopathic steroid resistant	Associate	15780077, 25112471
Netherton Syndrome	Associate	15253708, 37014572
Pre Eclampsia	Associate	27052160, 28621045
Proteinuria	Associate	11562357, 15496146, 15954915, 16572591, 23982418, 25112471, 28621045, 32779421, 36847718
Renal Insufficiency	Associate	30691124, 33305316, 40543848
Renal Insufficiency Chronic	Associate	31257514, 37510393
Sarcoma Kaposi	Associate	22578956
Segmental glomerulosclerosis	Associate	16572591
Uniparental Disomy	Associate	40543848
Uniparental disomy of chromosome 2	Associate	40543848
Wilms Tumor	Associate	37904849

NPHS2 (NPHS2 stomatin family member, podocin)