NPHS2 (NPHS2 stomatin family member, podocin)

Gene

• Entrez ID: 7827
• Gene name: NPHS2 stomatin family member, podocin
• Gene symbol: NPHS2
• Synonyms: PDCN, SRN1
• Chromosome: 1
• Chromosome location: 1q25.2
• 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]

SNPs

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

miRNA

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

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	12424224, 17675666, 22662192
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005886	Component	Plasma membrane	IBA	21873635
GO:0005886	Component	Plasma membrane	TAS
GO:0005887	Component	Integral component of plasma membrane	TAS	10742096
GO:0005911	Component	Cell-cell junction	IDA	17675666
GO:0007588	Process	Excretion	TAS	10742096
GO:0031235	Component	Intrinsic component of the cytoplasmic side of the plasma membrane	IDA	11786407
GO:0031532	Process	Actin cytoskeleton reorganization	IDA	17675666
GO:0032991	Component	Protein-containing complex	IDA	17675666
GO:0036057	Component	Slit diaphragm	IDA	11786407
GO:0045121	Component	Membrane raft	IDA	17675666
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145
GO:0072249	Process	Metanephric glomerular visceral epithelial cell development	IEP	11786407

Other IDs

• MIM: 604766
• HGNC: 13394
• e!Ensembl: 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

• Sequence:

  MERRARSSSRESRGRGGRTPHKENKRAKAERSGGGRGRQEAGPEPSGSGRAGTPGEPRAP
  AATVVDVDEVRGSGEEGTEVVALLESERPEEGTKSSGLGACEWLLVLISLLFIIMTFPFS
  IWFCVKVVQEYERVIIFRLGHLLPGRAKGPGLFFFLPCLDTYHKVDLRLQTLEIPFHEIV
  TKDMFIMEIDAICYYRMENASLLLSSLAHVSKAVQFLVQTTMKRLLAHRSLTEILLERKS
  IAQDAKVALDSVTCIWGIKVERIEIKDVRLPAGLQHSLAVEAEAQRQAKVRMIAAEAEKA
  ASESLRMAAEILSGTPAAVQLRYLHTLQSLSTEKPSTVVLPLPFDLLNCLSSPSNRTQGS
  LPFPSPSKPVEPLNPKKKDSPML

• Sequence length: 383

Pathways

Reactome:

Nephrin family interactions

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Alport syndrome, x-linked	Alport Syndrome, X-Linked	rs104886229, rs104886121, rs104886091, rs104886043, rs104886303, rs104886308, rs104886050, rs104886047, rs281874669, rs281874722, rs104886414, rs281874755, rs104886429, rs104886431, rs104886059, rs104886060, rs104886061, rs104886434, rs104886063, rs281874759, rs104886066, rs104886440, rs281874763, rs104886071, rs104886073, rs281874768, rs104886079, rs104886082, rs104886086, rs104886088, rs104886092, rs104886096, rs104886094, rs104886107, rs281874659, rs104886100, rs104886101, rs104886111, rs104886112, rs104886319, rs104886113, rs104886116, rs281874667, rs281874668, rs104886118, rs281874670, rs104886122, rs281874673, rs104886129, rs281874674, rs281874675, rs104886130, rs104886131, rs104886142, rs104886144, rs104886147, rs104886153, rs104886157, rs104886341, rs104886167, rs104886344, rs104886163, rs281874688, rs281874689, rs104886174, rs104886183, rs104886356, rs281874696, rs104886185, rs281874697, rs104886188, rs104886189, rs281874703, rs104886363, rs104886195, rs104886371, rs104886374, rs104886210, rs104886214, rs104886217, rs104886213, rs104886219, rs104886221, rs281874712, rs104886225, rs281874713, rs104886228, rs104886388, rs104886236, rs104886244, rs104886251, rs104886253, rs104886255, rs104886261, rs281874724, rs1556453243, rs104886269, rs587776402, rs587776403, rs104886276, rs104886279, rs104886413, rs104886293, rs281874743, rs104886287, rs104886288, rs281874747, rs104886298, rs104886302, rs281874753, rs104886306, rs281874738, rs281874761, rs281874671, rs397515496, rs797045035, rs869025333, rs869025334, rs104886338, rs869025331, rs869025332, rs878853089, rs878853114, rs886039890, rs886039886, rs1057516187, rs1057516203, rs1060499694, rs1060499710, rs1556451235, rs1131691795, rs1131692246, rs1556403112, rs1556404985, rs1556407064, rs281874702, rs104886282, rs1556411631, rs1556404027, rs1556407078, rs1556453276, rs1556419850, rs1556405010, rs1556405926, rs1556406001, rs1556406859, rs1556410516, rs1556419831, rs1556419869, rs1556419895, rs1556420349, rs1556420358, rs1556439394, rs1569509234, rs1569505374, rs1569505771, rs760109866, rs104886074, rs1569489353, rs1569490592, rs1569489328, rs1569505604, rs1569507535, rs1569469409, rs1569488426, rs1569488434, rs1569488437, rs767619131, rs104886054, rs104886443, rs1569491107, rs1569491399, rs1569491718, rs1210495852, rs1569493670, rs1569494267, rs867625069, rs886041509, rs1569497776, rs104886368, rs104886372, rs1569498896, rs1569505758, rs606231372, rs1569509257, rs1569490379, rs1569490932, rs1569492147, rs1569494061, rs1569494304, rs1569497690, rs1569498623, rs1569504056, rs1569505613, rs1569499015, rs1569493662, rs1569508360, rs1569497030, rs1569504068, rs1603290169, rs1603292422, rs1603297305, rs1603310370, rs104886235, rs1603310380, rs1603323174, rs104886424, rs1603279819, rs1603293624, rs1603278993, rs1603290131, rs1603279005, rs281874684, rs1603293639, rs1603328372, rs1556446493, rs1603323278, rs1603276159, rs1603276180, rs1603282474, rs1603287820, rs759179999, rs1603290148, rs1603290199, rs1603290681, rs281874683, rs1603291770, rs1603292021, rs1603293553, rs1603293570, rs1603293605, rs1291655627, rs1603297334, rs1603311030, rs1603323355, rs1603326397, rs104886078, rs1603326561, rs281874734, rs1603283567, rs1603286154, rs1603290763, rs1603290796, rs770451831, rs1603298378, rs1603298869, rs1603298993, rs1603306716, rs1603306718, rs1603318143, rs1603318154, rs1603328025, rs104886190, rs2068061224, rs750941179, rs2068718016, rs2067083148, rs2066231013, rs2066342176, rs1569494281, rs2068082287, rs2068126851, rs2068537554	26138234
Alport syndrome	Alport Syndrome, Autosomal Dominant, Alport Syndrome, Autosomal Recessive	rs104886303, rs121912858, rs121912859, rs121912860, rs121912861, rs121912862, rs121912824, rs121912825, rs1325453230, rs121912826, rs267606745, rs104886440, rs104886071, rs104886079, rs104886101, rs281874670, rs281874673, rs104886142, rs104886189, rs104886210, rs104886247, rs104886286, rs281874753, rs267599231, rs876657397, rs1553676221, rs1057519376, rs1057519377, rs201697532, rs374815903, rs200287952, rs1057516204, rs200672668, rs375040636, rs1060499654, rs1114167371, rs1131691738, rs1553627655, rs1363277825, rs1553690565, rs1175052474, rs748901402, rs1553641611, rs1189502123, rs534522842, rs1553683757, rs375450996, rs745672795, rs1553759430, rs868002181, rs756231749, rs35138315, rs1553764454, rs371334239, rs1553611876, rs1553612433, rs1553622675, rs1553625684, rs1553639043, rs773515249, rs1553760558, rs1556420349, rs1553612309, rs1206142672, rs369922627, rs1553624127, rs778043831, rs1553641728, rs768003309, rs1553643669, rs1553644402, rs1553658892, rs954701825, rs1553669704, rs779930511, rs926605269, rs1553612499, rs891854419, rs755927061, rs762518741, rs775373641, rs1553751122, rs1553611947, rs988439345, rs1274459294, rs1553755124, rs772958162, rs1553755767, rs993103826, rs1196996393, rs1553762113, rs749383170, rs1446915781, rs1553682895, rs1553683192, rs1489351299, rs1553688712, rs748473278, rs1553690604, rs1553696207, rs937550597, rs1553611909, rs1203564054, rs773081522, rs1491486533, rs1553688330, rs1553753119, rs1422638161, rs754669149, rs1553712110, rs1553757096, rs1396602090, rs1553758919, rs1553762314, rs202001097, rs749390823, rs1553750900, rs1346138010, rs1553765265, rs1369097739, rs1469479748, rs748026887, rs1553766404, rs1444785718, rs1553760257, rs766306957, rs371172166, rs766900945, rs1553762279, rs769783985, rs201648982, rs1553762936, rs781566652, rs769863513, rs867868993, rs760846085, rs1351781261, rs1553676230, rs1553681714, rs1553688696, rs1201925443, rs1553725815, rs1553750572, rs1553751120, rs1553752199, rs756133651, rs1158937060, rs1553758893, rs1553759476, rs1306992119, rs1553759665, rs1440033157, rs1553760802, rs1445615417, rs759873621, rs1553766735, rs1559617617, rs1026613471, rs1559882199, rs1559395617, rs772708743, rs1040287646, rs1241404192, rs1559873550, rs1569492951, rs1569494378, rs1559394354, rs1559455617, rs1559563141, rs1559563525, rs1559594442, rs1559606445, rs1559620132, rs1005389790, rs923865420, rs1559644463, rs1559646395, rs1559890352, rs983885088, rs1559909384, rs1559914770, rs1559628183, rs368434069, rs1559913871, rs1559878862, rs1575895541, rs1569492161, rs1574803132, rs1271416659, rs1575714693, rs1576207007, rs1576428862, rs1576457876, rs760795817, rs1574699806, rs779575469, rs1399954090, rs1574813382, rs1574823172, rs1574823188, rs1574813350, rs1574658390, rs1576129421, rs1574782406, rs1453590085, rs750308686, rs1574701767, rs1574728278, rs1574786225, rs1603290681, rs1574698507, rs750345987, rs1574767962, rs141127013, rs1575696646, rs1003748020, rs1576571835, rs1576812577, rs1207493576, rs1574681401, rs1363441287, rs1247804051, rs1574745989, rs1574782666, rs1402894646, rs746766677, rs1574803208, rs1305836268, rs2073752422, rs2071916145, rs1974295317, rs759043857, rs2073446714, rs1363058249	26138234
Hematuria	Hematuria, Benign Familial	rs104886308, rs1131692060, rs1306992119	26138234
Hyperlipidemia	Hyperlipidemia	rs118204057, rs118204060, rs118204062, rs1563569634, rs118204069, rs118204070, rs118204071, rs3737787, rs2073658, rs1566946168, rs1064797075
Kidney disease	Chronic kidney disease stage 5	rs74315342, rs749740335, rs757649673, rs112417755, rs35138315
Nephrotic syndrome	Nephrotic Syndrome, Idiopathic Nephrotic Syndrome	rs876657369, rs121912601, rs121912602, rs876657370, rs121912603, rs121912604, rs121912605, rs121907900, rs121907901, rs28941778, rs587776576, rs28942089, rs587776577, rs28941777, rs121907910, rs1568296260, rs119473033, rs74315342, rs74315343, rs74315345, rs74315346, rs74315347, rs74315348, rs121434394, rs267606919, rs121912488, rs267606953, rs267606954, rs267606955, rs104886210, rs1591732280, rs1591750243, rs140511594, rs140781106, rs147972030, rs587776969, rs386833863, rs386833880, rs386833882, rs386833892, rs386833895, rs386833909, rs386833911, rs386833920, rs386833935, rs386833947, rs1555763603, rs398122978, rs398122979, rs398122980, rs369573693, rs398122981, rs398122982, rs398122983, rs200482683, rs730882194, rs180177201, rs587777552, rs587777553, rs775170915, rs749740335, rs12568913, rs530318579, rs786204583, rs786204708, rs786204632, rs138656762, rs797044992, rs797044994, rs797044995, rs864321632, rs864321687, rs864321688, rs864321633, rs869025495, rs869025541, rs869312747, rs145473779, rs757674160, rs869320695, rs138909849, rs869312984, rs1057516900, rs763818901, rs199506378, rs1057517164, rs1057516523, rs1057516414, rs778055996, rs1057516395, rs1057516747, rs1057516880, rs1057516680, rs778217926, rs1057519347, rs764587648, rs1060499703, rs121907903, rs769259446, rs1131692252, rs1131692253, rs1131692254, rs1131692255, rs1131692256, rs746887949, rs1131692235, rs1135402911, rs1135402912, rs1135402913, rs1554946480, rs1555331969, rs773173317, rs1555816634, rs775006954, rs1320543506, rs534522842, rs1272948499, rs1191455921, rs1291398331, rs1554939785, rs776016942, rs1031744496, rs748812981, rs755972674, rs1553312833, rs967339926, rs1462028977, rs1212702104, rs1167223941, rs762631237, rs1553316575, rs1553315173, rs1553316648, rs1553316611, rs780761368, rs368572297, rs1568070817, rs1321552081, rs1558108130, rs1558091788, rs1565707103, rs1558355124, rs1564622701, rs1351580598, rs1589475328, rs1589413498, rs1572255744, rs1572262824, rs761410195, rs1602413491, rs1590326226, rs375998390, rs570583897, rs369363545, rs201488687, rs1334894971, rs763782471, rs138047529, rs895782232, rs1572255047, rs1589433172, rs1589509476, rs1572277600, rs1572282458, rs1584675898, rs759043857, rs1853443391	16898497, 26420286, 15253708, 15322893, 21415313, 12649741, 15496146, 15327385, 19674119, 11805166, 29382718, 17899208, 23913389, 24227627, 24072147, 24509478, 22578956, 21355056, 15769810, 23013956, 12464671, 18596732, 24742477, 24500309, 25525159, 10742096, 23242530, 28117080, 25349199, 19067903, 11729243, 21171529, 14978175, 14675423, 11805168, 22565185, 18216321, 20947785, 15780077, 20798252, 15015071, 21636722, 23645318, 16810518, 20507940, 23800802, 15817495, 16721582, 25852895, 23595123, 19406966, 26413278, 12707396, 24856380, 26138234, 20001346, 23515051, 11854170, 19145239, 25599733, 11733557, 19371226, 26668027, 28204945, 18823551, 18443213

Unknown
Disease name	Disease term	dbSNP ID	References
Genetic steroid-resistant nephrotic syndrome	Genetic steroid-resistant nephrotic syndrome
Glomerular hyalinosis	Hyalinosis, Segmental Glomerular		15942677
Glomerulosclerosis	Focal glomerulosclerosis		15942677
Hypertensive nephropathy	hypertensive nephropathy
Hypoalbuminemia	Hypoalbuminemia
Nephritis	NEPHROTIC SYNDROME, STEROID-RESISTANT, AUTOSOMAL RECESSIVE		22578956, 21171529, 16810518, 15769810, 20507940, 15817495, 25349199, 23645318, 14675423, 17899208, 28117080, 11805166, 18443213, 24072147, 15322893, 14978175, 15327385, 23595123, 19406966, 15496146, 23242530, 24500309, 11805168, 15015071, 11854170, 24227627, 12707396, 11729243, 25852895, 11733557, 19674119, 29382718, 20798252, 24509478, 25599733, 21636722, 20947785, 23013956, 18216321, 22565185, 18596732, 26138234, 25525159, 26413278, 18823551, 10742096, 24856380, 28204945, 16721582, 23515051, 15253708, 15780077, 19371226, 21355056, 19067903, 20001346, 19145239, 12464671, 12649741, 26668027
Nephrosis	Nephrosis		15684566
Renal glomerular disease	Renal glomerular disease