NPHS2 (Podocin) variants and mutations
NPHS2 (also known as Podocin) is a human protein-coding gene encoding a podocin protein. It organizes nephrin-containing slit-diaphragm complexes in podocytes and helps maintain the glomerular filtration barrier. Biallelic pathogenic variants are a major cause of steroid-resistant nephrotic syndrome and focal segmental glomerulosclerosis. This analysis covers 763 NPHS2 variants and mutations. Of these, 79% have computational variant effect predictions. Disease context includes nephrotic syndrome, nephrotic syndrome, type 2, and familial idiopathic steroid-resistant nephrotic syndrome. Example NPHS2 variants include M1I, M1L, and E2D.
Variant analysis overview
- Gene: NPHS2
- Protein: Podocin
- UniProt accession: Q9NP85
- Organism: Homo sapiens
- Variants analyzed: 763
- Variant scope: all variants
- Completed: 2026-08-19
Variant and mutation evidence
- Variant composition: 550 unspecified-consequence records; 88 missense variants; 93 synonymous variants; 11 frameshift variants; 3 in-frame deletions; 1 in-frame insertions; 5 stop-gained variants; 5 splice-region variants; 7 substitution
- Prediction scores: 599 variants have prediction scores (79% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: nephrotic syndrome, nephrotic syndrome, type 2, familial idiopathic steroid-resistant nephrotic syndrome, steroid-resistant nephrotic syndrome, idiopathic nephrotic syndrome, focal segmental glomerulosclerosis, hereditary disease, Nephrotic range proteinuria, congenital nephrotic syndrome, Finnish type, Proteinuria, gout, chronic kidney disease.
Protein structure and variant hotspots
- Protein features: 1 post-translational modification sites.
- PTM context: 2 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, AlphaFold DB, gnomAD constraint, Open Targets, MaveDB, LitVar.
Notable NPHS2 variants
Examples include M1I, M1L, E2D, R3G, R3K, R3S, R4K, A5E. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1I (p.Met1Ile), rs1057516680, ClinGen CA16040673, ClinVar RCV000409834, ClinGen CA343554473, MetaLR 0.99, MetaSVM 1.17, Pathogenic, not provided
- M1L (p.Met1Leu), rs2101887841, ClinGen CA343554484, ClinVar RCV001849816, ClinVar RCV002250777, MetaLR 0.99, MetaSVM 1.08, Pathogenic, Nephrotic syndrome, type 2
- E2D (p.Glu2Asp), ExAC rs766878036, gnomAD rs766878036, REVEL 0.36, CADD 15.90
- R3G (p.Arg3Gly), UniProt VAR 072134, REVEL 0.59, CADD 23.50, Pathogenic, in NPHS2
- R3K (p.Arg3Lys), TOPMed rs1674751079, REVEL 0.36, CADD 4.05
- R3S (p.Arg3Ser), TOPMed rs1355832790, gnomAD rs1355832790, REVEL 0.45, CADD 13.30
- R4K (p.Arg4Lys), TOPMed rs1031260460, gnomAD rs1031260460, REVEL 0.41, CADD 12.70
- A5E (p.Ala5Glu), TOPMed rs1213377429, gnomAD rs1213377429, REVEL 0.48, CADD 22.90
- A5G (p.Ala5Gly), TOPMed rs1213377429, gnomAD rs1213377429, REVEL 0.44, CADD 22.00
- A5V (p.Ala5Val), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10085, TOPMed rs1213377429, gnomAD rs1213377429, REVEL 0.46, CADD 23.00, Variant assessed as somatic; moderate impact.
- R6G (p.Arg6Gly), gnomAD rs1449925481
- R6Q (p.Arg6Gln), rs760885607, ClinGen CA1267338, cosmic curated COSV10528, ClinVar RCV001098018, REVEL 0.47, CADD 25.30, Uncertain significance, not provided; Nephrotic syndrome, type 2
- S7R (p.Ser7Arg), ExAC rs750515960, TOPMed rs750515960, gnomAD rs750515960, REVEL 0.52, CADD 24.00, Likely benign
- S8F (p.Ser8Phe), TOPMed rs1265598373, gnomAD rs1265598373, REVEL 0.49, CADD 22.80
- R10K (p.Arg10Lys), TOPMed rs920479356, gnomAD rs920479356, REVEL 0.50, CADD 23.20, Uncertain significance
- R10S (p.Arg10Ser), ExAC rs767916334, gnomAD rs767916334, REVEL 0.59, CADD 12.60
- R10T (p.Arg10Thr), rs920479356, ClinGen CA33654147, ClinVar RCV003226802, ClinVar RCV005012816, REVEL 0.71, CADD 23.20, Uncertain significance, Nephrotic syndrome, type 2; not specified
- E11K (p.Glu11Lys), cosmic curated COSV10085, 1000Genomes rs532992157, REVEL 0.43, CADD 16.90
- S12F (p.Ser12Phe), 1000Genomes rs2101887766, REVEL 0.39, CADD 20.40
- R13L (p.Arg13Leu), 1000Genomes rs564179614, ExAC rs564179614, gnomAD rs564179614, REVEL 0.34, CADD 0.29
- R13S (p.Arg13Ser), Ensembl rs866704941, REVEL 0.44, CADD 15.20
- G14R (p.Gly14Arg), cosmic curated COSV10970, TOPMed rs973602590, gnomAD rs973602590, REVEL 0.36, CADD 3.53, Uncertain significance, Nephrotic syndrome, type 2
- R15* (p.Arg15Ter), cosmic curated COSV10889, Ensembl rs1674747229, CADD 34.00
- R15L (p.Arg15Leu), gnomAD rs1347576607, REVEL 0.42, CADD 17.10
- R15Q (p.Arg15Gln), gnomAD rs1347576607, REVEL 0.35, CADD 16.80
- G16C (p.Gly16Cys), Ensembl rs868756536, REVEL 0.46, CADD 11.60
- G17A (p.Gly17Ala), rs2526380257, ClinVar RCV004574394, Likely pathogenic
- R18T (p.Arg18Thr), UniProt VAR 072135, REVEL 0.38, CADD 10.80, Pathogenic, in NPHS2
- T19P (p.Thr19Pro), TOPMed rs1442129751, gnomAD rs1442129751, REVEL 0.27, CADD 0.14, Uncertain significance, Nephrotic syndrome, type 2
- P20L (p.Pro20Leu), rs74315344, ClinGen CA117451, ClinVar RCV000005696, ClinVar RCV000588524, REVEL 0.61, CADD 16.70, Conflicting interpretations, not specified; not provided; Finnish congenital nephrotic syndrome
- P20S (p.Pro20Ser), TOPMed rs1330347011, gnomAD rs1330347011, REVEL 0.20, CADD 0.82
- K22N (p.Lys22Asn), ExAC rs768283220, TOPMed rs768283220, gnomAD rs768283220, REVEL 0.21, CADD 9.91
- R26K (p.Arg26Lys), cosmic curated COSV10528, 1000Genomes rs530691832, ExAC rs530691832, REVEL 0.18, CADD 1.67
- R26M (p.Arg26Met), UniProt VAR 072136, REVEL 0.61, CADD 12.90, Pathogenic, in NPHS2
- A27G (p.Ala27Gly), TOPMed rs1455419528, gnomAD rs1455419528, REVEL 0.21, CADD 6.50
- A27T (p.Ala27Thr), TOPMed rs1167176148, REVEL 0.23, CADD 6.84
- K28M (p.Lys28Met), rs1340195940, UniProt VAR 072137, TOPMed rs1340195940, gnomAD rs1340195940, REVEL 0.62, CADD 22.30, Pathogenic, in NPHS2
- K28Q (p.Lys28Gln), gnomAD rs1674744920, REVEL 0.47, CADD 17.80
- A29T (p.Ala29Thr), rs561887984, ClinGen CA1267332, ClinVar RCV000668713, UniProt VAR 071212, REVEL 0.56, CADD 12.80, Uncertain significance, Nephrotic syndrome, type 2
- E30* (p.Glu30Ter), TOPMed rs1477180313, gnomAD rs1477180313, CADD 35.00, Uncertain significance, in NPHS2
- E30D (p.Glu30Asp), TOPMed rs1234623184, gnomAD rs1234623184, REVEL 0.40, CADD 5.98, Likely benign, in NPHS2
- E30K (p.Glu30Lys), rs1477180313, ClinGen CA343554016, ClinVar RCV000671814, UniProt VAR 072138, REVEL 0.60, CADD 11.10, Uncertain significance, Nephrotic syndrome, type 2
- E30Q (p.Glu30Gln), UniProt VAR 072139, Pathogenic, in NPHS2
- R31M (p.Arg31Met), gnomAD rs1205324277, REVEL 0.41, CADD 14.30
- R31S (p.Arg31Ser), gnomAD rs1437690215, REVEL 0.35, CADD 14.20, Likely benign
- S32N (p.Ser32Asn), TOPMed rs1273099099, gnomAD rs1273099099, REVEL 0.24, CADD 4.17
- S32R (p.Ser32Arg), rs886043653, ClinGen CA10605787, ClinVar RCV000343887, TOPMed rs886043653, REVEL 0.28, CADD 11.40, Uncertain significance, Inborn genetic diseases
- G33D (p.Gly33Asp), gnomAD rs1280112779, REVEL 0.34, CADD 8.20
- G33S (p.Gly33Ser), gnomAD rs1349015771, REVEL 0.20, CADD 2.37
- G34E (p.Gly34Glu), rs1674742844, UniProt VAR 071213, TOPMed rs1674742844, REVEL 0.40, CADD 1.85
- G34R (p.Gly34Arg), TOPMed rs1033965843, gnomAD rs1033965843, REVEL 0.43, CADD 1.85
- G35D (p.Gly35Asp), rs878853215, ClinGen CA10581522, ClinVar RCV000225091, gnomAD rs878853215, REVEL 0.22, CADD 5.84, drug response, Prednisolone response
- G35S (p.Gly35Ser), ExAC rs746606967, TOPMed rs746606967, gnomAD rs746606967, REVEL 0.24, CADD 1.97, Uncertain significance, Nephrotic syndrome, type 2
- G35V (p.Gly35Val), gnomAD rs878853215, REVEL 0.24, CADD 5.42, Uncertain significance, Nephrotic syndrome, type 2
- R36H (p.Arg36His), ExAC rs755338607, REVEL 0.39, CADD 22.00
- R36S (p.Arg36Ser), ExAC rs779357846, REVEL 0.25, CADD 15.80
- G37E (p.Gly37Glu), ExAC rs750532480, TOPMed rs750532480, gnomAD rs750532480, REVEL 0.29, CADD 8.77
- G37R (p.Gly37Arg), ExAC rs756683527, gnomAD rs756683527, REVEL 0.34, CADD 8.39
- G37V (p.Gly37Val), ExAC rs750532480, TOPMed rs750532480, gnomAD rs750532480
- G37W (p.Gly37Trp), ExAC rs756683527, gnomAD rs756683527, REVEL 0.33, CADD 17.50
- R38C (p.Arg38Cys), ExAC rs767644222, TOPMed rs767644222, gnomAD rs767644222, REVEL 0.35, CADD 18.20
- R38G (p.Arg38Gly), ExAC rs767644222, TOPMed rs767644222, gnomAD rs767644222, REVEL 0.32, CADD 11.40
- R38H (p.Arg38His), ExAC rs762145203, TOPMed rs762145203, gnomAD rs762145203, REVEL 0.28, CADD 1.88
- R38L (p.Arg38Leu), ExAC rs762145203, TOPMed rs762145203, gnomAD rs762145203, REVEL 0.32, CADD 0.89, Uncertain significance, Inborn genetic diseases
- R38P (p.Arg38Pro), ExAC rs762145203, TOPMed rs762145203, gnomAD rs762145203, REVEL 0.28, CADD 2.18
- R38S (p.Arg38Ser), ExAC rs767644222, TOPMed rs767644222, gnomAD rs767644222, REVEL 0.32, CADD 8.07
- Q39* (p.Gln39Ter), rs869312746, ClinGen CA354118, ClinVar RCV000210047, Ensembl rs869312746, Uncertain significance, in NPHS2
- Q39L (p.Gln39Leu), UniProt VAR 072140, Pathogenic, in NPHS2
- Q39P (p.Gln39Pro), TOPMed rs1410441966, gnomAD rs1410441966, REVEL 0.21, CADD 5.84
- Q39R (p.Gln39Arg), TOPMed rs1410441966, gnomAD rs1410441966, REVEL 0.21, CADD 3.13
- E40* (p.Glu40Ter), rs751695916, ExAC rs751695916, CADD 35.00, Variant assessed as somatic; high impact.
- E40G (p.Glu40Gly), Ensembl rs2101887492, REVEL 0.31, CADD 15.00
- A41G (p.Ala41Gly), rs762708477, ClinGen CA1267315, ClinVar RCV002962192, ExAC rs762708477, REVEL 0.31, CADD 9.67, Uncertain significance, not provided
- A41S (p.Ala41Ser), rs764350609, ClinGen CA1267316, ClinVar RCV002909879, ClinVar RCV003358021, REVEL 0.26, CADD 3.31, Uncertain significance, Inborn genetic diseases; not provided
- A41T (p.Ala41Thr), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10085, Variant assessed as somatic; moderate impact.
- G42R (p.Gly42Arg), rs559836164, ClinGen CA1267314, ClinVar RCV000665608, ClinVar RCV000883029, REVEL 0.56, CADD 2.69, Benign/Likely benign, Nephrotic syndrome, type 2; not provided
- P43A (p.Pro43Ala), 1000Genomes rs545872093, Pathogenic
- E44* (p.Glu44Ter), rs759402903, ClinGen CA343553635, ClinVar RCV003881108, ExAC rs759402903, CADD 33.00, Pathogenic
- E44A (p.Glu44Ala), UniProt VAR 071214
- E44K (p.Glu44Lys), ExAC rs759402903, TOPMed rs759402903, gnomAD rs759402903, REVEL 0.23, CADD 7.58, Pathogenic
- P45R (p.Pro45Arg), ExAC rs770379901, gnomAD rs770379901, REVEL 0.22, CADD 0.11
- P45T (p.Pro45Thr), Ensembl rs2101887423, REVEL 0.23, CADD 8.50
- S46* (p.Ser46Ter), gnomAD rs1327842593, CADD 34.00
- S46L (p.Ser46Leu), gnomAD rs1327842593, REVEL 0.17, CADD 7.24
- S46W (p.Ser46Trp), gnomAD rs1327842593, REVEL 0.37, CADD 15.00
- S48Y (p.Ser48Tyr), rs886042865, ClinGen CA10604789, ClinVar RCV000395550, Ensembl rs886042865, REVEL 0.28, CADD 10.80, Uncertain significance, not provided
- G49A (p.Gly49Ala), TOPMed rs1674736597
- R50G (p.Arg50Gly), TOPMed rs886045596, gnomAD rs886045596, REVEL 0.38, CADD 9.73, Likely benign
- R50P (p.Arg50Pro), gnomAD rs1246051609, REVEL 0.40, CADD 11.70
- R50W (p.Arg50Trp), rs886045596, ClinGen CA10608825, ClinVar RCV000297548, ClinVar RCV004021379, REVEL 0.42, CADD 16.40, Uncertain significance, Inborn genetic diseases; Nephrotic syndrome, type 2
- A51L (p.Ala51Leu), rs2526378384, ClinGen CA2580061521, ClinVar RCV003086446, Uncertain significance, not provided
- A51P (p.Ala51Pro), TOPMed rs911929132, gnomAD rs911929132, REVEL 0.31, CADD 6.54
- A51S (p.Ala51Ser), TOPMed rs911929132, gnomAD rs911929132
- A51T (p.Ala51Thr), TOPMed rs911929132, gnomAD rs911929132, REVEL 0.24, CADD 3.56
- A51V (p.Ala51Val), TOPMed rs1050414387, gnomAD rs1050414387, REVEL 0.28, CADD 9.68
- G52E (p.Gly52Glu), NCI-TCGA TCGA novel, REVEL 0.17, CADD 0.64, Variant assessed as somatic; moderate impact.
- G52R (p.Gly52Arg), Ensembl rs1674735731
- T53P (p.Thr53Pro), rs932902995, ClinGen CA33653862, ClinVar RCV002798133, Ensembl rs932902995, REVEL 0.39, CADD 12.20, Uncertain significance, Inborn genetic diseases
- P54L (p.Pro54Leu), TOPMed rs1400380943, gnomAD rs1400380943, REVEL 0.18, CADD 9.51
- P54R (p.Pro54Arg), TOPMed rs1400380943, gnomAD rs1400380943, REVEL 0.24, CADD 7.72
- G55A (p.Gly55Ala), TOPMed rs1674734678
- G55R (p.Gly55Arg), TOPMed rs1409794630, gnomAD rs1409794630, REVEL 0.22, CADD 5.81, Uncertain significance, Nephrotic syndrome, type 2
- G55W (p.Gly55Trp), TOPMed rs1409794630, gnomAD rs1409794630, REVEL 0.43, CADD 14.90
- E56* (p.Glu56Ter), rs1167223941, ClinGen CA343553305, ClinVar RCV000671272, ClinVar RCV003688873, CADD 35.00, Pathogenic
- E56G (p.Glu56Gly), rs749680357, ClinGen CA1267306, ClinVar RCV001757813, ExAC rs749680357, AlphaMissense 0.07, MetaLR 0.95, Uncertain significance, not provided
- E56K (p.Glu56Lys), rs1167223941, NCI-TCGA Cosmic COSV6263, cosmic curated COSV62635, gnomAD rs1167223941, REVEL 0.40, CADD 15.60, Pathogenic
- P57T (p.Pro57Thr), gnomAD rs1417783121, REVEL 0.28, CADD 10.90
- A59E (p.Ala59Glu), rs201106340, ClinGen CA1267303, ClinVar RCV002193009, 1000Genomes rs201106340, REVEL 0.37, CADD 16.40, Likely benign, not provided
- A59P (p.Ala59Pro), ExAC rs756699855, gnomAD rs756699855, REVEL 0.43, CADD 16.30
- A59V (p.Ala59Val), 1000Genomes rs201106340, ESP rs201106340, ExAC rs201106340, TOPMed rs201106340, REVEL 0.36, CADD 16.60, Likely benign
- A61T (p.Ala61Thr), rs757457347, ClinGen CA1267301, ClinVar RCV002629887, ClinVar RCV004072102, REVEL 0.31, CADD 18.00, Uncertain significance, not provided; Inborn genetic diseases
- A61V (p.Ala61Val), rs201050491, ClinGen CA1267300, cosmic curated COSV62635, ClinVar RCV000517708, REVEL 0.34, CADD 21.30, Benign/Likely benign, Nephrotic syndrome, type 2; not provided; not specified
- A62S (p.Ala62Ser), TOPMed rs1265632102, gnomAD rs1265632102, Uncertain significance
- A62T (p.Ala62Thr), rs1265632102, ClinGen CA343553199, ClinVar RCV002731692, TOPMed rs1265632102, REVEL 0.38, CADD 15.40, Uncertain significance, Inborn genetic diseases
- V64M (p.Val64Met), TOPMed rs1334989339, gnomAD rs1334989339, REVEL 0.39, CADD 23.30
- V65M (p.Val65Met), Ensembl rs1674732797, REVEL 0.48, CADD 24.40
- D66E (p.Asp66Glu), gnomAD rs1226582592, REVEL 0.35, CADD 13.20
- D66N (p.Asp66Asn), ExAC rs758645314, gnomAD rs758645314, REVEL 0.36, CADD 19.60
- V67L (p.Val67Leu), TOPMed rs1363776277, gnomAD rs1363776277, REVEL 0.37, CADD 20.40
- V67M (p.Val67Met), TOPMed rs1363776277, gnomAD rs1363776277, REVEL 0.39, CADD 23.10
- D68G (p.Asp68Gly), gnomAD rs1289258360, REVEL 0.49, CADD 24.60
- E69* (p.Glu69Ter), rs1434578927, ClinGen CA343553001, ClinVar RCV003689971, TOPMed rs1434578927, CADD 38.00, Pathogenic
- E69V (p.Glu69Val), ExAC rs752442249, gnomAD rs752442249, REVEL 0.38, CADD 22.60
- V70I (p.Val70Ile), ExAC rs764956573, TOPMed rs764956573, gnomAD rs764956573, REVEL 0.38, CADD 20.90, Uncertain significance, Inborn genetic diseases
- R71* (p.Arg71Ter), rs1462028977, ClinGen CA343552954, ClinVar RCV000664539, TOPMed rs1462028977, CADD 39.00, Pathogenic
- R71Q (p.Arg71Gln), gnomAD rs1417320743, REVEL 0.39, CADD 22.40
- G74D (p.Gly74Asp), ESP rs148976646, ExAC rs148976646, TOPMed rs148976646, REVEL 0.38, CADD 16.90
- G74R (p.Gly74Arg), cosmic curated COSV10970, ExAC rs200544576, TOPMed rs200544576, gnomAD rs200544576, Uncertain significance
- G74S (p.Gly74Ser), rs200544576, ClinGen CA1267294, NCI-TCGA Cosmic COSV6263, cosmic curated COSV62634, REVEL 0.33, CADD 18.30, Uncertain significance, not provided; NPHS2-related disorder; Inborn genetic diseases
- E75K (p.Glu75Lys), rs760160509, ClinGen CA1267292, cosmic curated COSV62636, ClinVar RCV004491024, REVEL 0.37, CADD 22.80, Uncertain significance, Inborn genetic diseases
- E76* (p.Glu76Ter), TOPMed rs1674730598, CADD 38.00
- G77C (p.Gly77Cys), TOPMed rs1186309031, gnomAD rs1186309031, REVEL 0.44, CADD 24.00
- G77S (p.Gly77Ser), TOPMed rs1186309031, gnomAD rs1186309031, REVEL 0.37, CADD 21.50
- E79K (p.Glu79Lys), ExAC rs772773926, TOPMed rs772773926, gnomAD rs772773926, REVEL 0.64, CADD 23.50
- V81G (p.Val81Gly), gnomAD rs1264389932, REVEL 0.34, CADD 20.70
- A82R (p.Ala82Arg), rs2526376882, ClinGen CA2580061516, ClinVar RCV002306986, Likely pathogenic
- A82T (p.Ala82Thr), TOPMed rs959941569
- L84V (p.Leu84Val), Ensembl rs1572299422
- E85K (p.Glu85Lys), rs771625593, ClinGen CA1267289, ClinVar RCV001303724, ExAC rs771625593, REVEL 0.47, CADD 23.00, Uncertain significance, not provided
- S86R (p.Ser86Arg), rs2526376498, ClinGen CA2582342426, ClinVar RCV003340977, REVEL 0.58, CADD 22.30, Likely pathogenic
- E87* (p.Glu87Ter), rs776016821, ClinGen CA343552591, ClinVar RCV001174946, ClinVar RCV001828589, CADD 39.00, Pathogenic
- E87K (p.Glu87Lys), ExAC rs776016821, TOPMed rs776016821, gnomAD rs776016821, REVEL 0.59, CADD 23.00, Pathogenic
- E87Q (p.Glu87Gln), ExAC rs776016821, TOPMed rs776016821, gnomAD rs776016821, REVEL 0.47, CADD 22.50, Pathogenic
- E87V (p.Glu87Val), gnomAD rs1248610544, REVEL 0.62, CADD 24.60
- R88L (p.Arg88Leu), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10085, Variant assessed as somatic; moderate impact.
- R88Q (p.Arg88Gln), Ensembl rs1674728356, REVEL 0.25, CADD 19.20
- P89H (p.Pro89His), NCI-TCGA Cosmic COSV6263, REVEL 0.33, CADD 17.60, Variant assessed as somatic; moderate impact., in NPHS2
- P89L (p.Pro89Leu), rs2526376552, ClinGen CA343552497, ClinVar RCV004491025, ClinVar RCV005610672, REVEL 0.28, CADD 17.60, Uncertain significance, Inborn genetic diseases
- P89T (p.Pro89Thr), UniProt VAR 072141, REVEL 0.68, CADD 16.30, Pathogenic, in NPHS2
- E90K (p.Glu90Lys), cosmic curated COSV10652, gnomAD rs1441982526, REVEL 0.49, CADD 23.60
- E90R (p.Glu90Arg), rs761298708, ClinGen CA1267286, ClinVar RCV002474422, Likely pathogenic
- E91G (p.Glu91Gly), Ensembl rs76150581
- E91K (p.Glu91Lys), NCI-TCGA Cosmic COSV6263, cosmic curated COSV62635, REVEL 0.62, CADD 22.80, Variant assessed as somatic; moderate impact.
- G92C (p.Gly92Cys), rs74315345, ClinGen CA117454, NCI-TCGA Cosmic COSV6263, cosmic curated COSV62635, AlphaMissense 0.24, MetaLR 0.98, Pathogenic, Nephrotic syndrome, type 2
- G92R (p.Gly92Arg), gnomAD rs74315345, Pathogenic, in NPHS2
- G92S (p.Gly92Ser), rs74315345, ClinGen CA343552395, NCI-TCGA Cosmic COSV6263, REVEL 0.64, AlphaMissense 0.24, Uncertain significance, not provided
- G92V (p.Gly92Val), ESP rs142342448, ExAC rs142342448, TOPMed rs142342448, gnomAD rs142342448, REVEL 0.75, CADD 25.30, Uncertain significance, Nephrotic syndrome, type 2
- T93I (p.Thr93Ile), gnomAD rs1376724226, REVEL 0.31, CADD 9.19
- T93N (p.Thr93Asn), cosmic curated COSV62636, gnomAD rs1376724226
- T93P (p.Thr93Pro), TOPMed rs1250341232, gnomAD rs1250341232, REVEL 0.36, CADD 13.80
- S95F (p.Ser95Phe), rs1187796947, ClinGen CA343571128, NCI-TCGA Cosmic COSV1008, cosmic curated COSV10085, REVEL 0.48, CADD 24.00, Uncertain significance, not provided
- S96C (p.Ser96Cys), TOPMed rs1250680481, gnomAD rs1250680481, REVEL 0.54, CADD 24.00
- G97D (p.Gly97Asp), NCI-TCGA TCGA novel, TOPMed rs1674274310, Uncertain significance, in NPHS2
- G97R (p.Gly97Arg), rs200913299, ClinGen CA343571111, ClinVar RCV003069254, ClinVar RCV005002943, REVEL 0.34, CADD 17.80, Uncertain significance, Nephrotic syndrome, type 2; not provided
- G97S (p.Gly97Ser), rs200913299, ClinGen CA1267263, ClinVar RCV003051043, UniProt VAR 071216, REVEL 0.28, CADD 12.00, Uncertain significance, not provided
- L98F (p.Leu98Phe), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G99E (p.Gly99Glu), rs771349484, ClinGen CA1267262, ClinVar RCV002924364, ExAC rs771349484, REVEL 0.74, CADD 23.80, Uncertain significance, Inborn genetic diseases
- C101S (p.Cys101Ser), ExAC rs777738678, TOPMed rs777738678, gnomAD rs777738678, REVEL 0.78, AlphaMissense 0.49, Uncertain significance
- C101Y (p.Cys101Tyr), rs777738678, ClinGen CA343571059, ClinVar RCV001356520, ExAC rs777738678, AlphaMissense 0.49, MetaLR 0.97, Uncertain significance, not provided
- E102K (p.Glu102Lys), rs1553315157, ClinGen CA343571048, NCI-TCGA Cosmic COSV1008, cosmic curated COSV10085, AlphaMissense 0.70, MetaLR 0.99, Uncertain significance, not specified
- W103* (p.Trp103Ter), gnomAD rs1254468728, CADD 39.00
- W103L (p.Trp103Leu), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10085, Variant assessed as somatic; moderate impact.
- L104F (p.Leu104Phe), rs1674273482, ClinGen CA343571017, ClinVar RCV002647718, TOPMed rs1674273482, AlphaMissense 0.09, MetaLR 0.93, Uncertain significance, not provided
- L104I (p.Leu104Ile), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10085, Variant assessed as somatic; moderate impact.
- L105F (p.Leu105Phe), ExAC rs772151217, gnomAD rs772151217, REVEL 0.75, CADD 24.20
- V106F (p.Val106Phe), ExAC rs748196828, gnomAD rs748196828
- L107F (p.Leu107Phe), gnomAD rs1287838405, REVEL 0.37, CADD 14.10
- L107P (p.Leu107Pro), UniProt VAR 071217, Pathogenic, in NPHS2
- I108L (p.Ile108Leu), Ensembl rs1572286211
- S109F (p.Ser109Phe), rs267598209, NCI-TCGA Cosmic COSV6263, cosmic curated COSV62634, Ensembl rs267598209, AlphaMissense 0.30, MetaLR 0.98, Variant assessed as somatic; moderate impact.
Public NPHS2 analysis runs
- NPHS2 analysis run — NPHS2 (763 variants) — completed 2026-08-19