Incidental Mutation 'R1024:Nphs1'
ID 98752
Institutional Source Beutler Lab
Gene Symbol Nphs1
Ensembl Gene ENSMUSG00000006649
Gene Name nephrosis 1, nephrin
Synonyms nephrin
MMRRC Submission 039126-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1024 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 30157740-30186648 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 30173702 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Isoleucine at position 939 (S939I)
Ref Sequence ENSEMBL: ENSMUSP00000116500 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006825] [ENSMUST00000126297]
AlphaFold Q9QZS7
Predicted Effect probably damaging
Transcript: ENSMUST00000006825
AA Change: S953I

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: S953I

DomainStartEndE-ValueType
signal peptide 1 36 N/A INTRINSIC
IG 52 146 1.38e-6 SMART
Pfam:C2-set_2 152 242 4.1e-20 PFAM
IG 264 351 9.86e-3 SMART
IG_like 360 452 2.73e1 SMART
IG 464 556 2.99e-2 SMART
IG_like 572 644 8.9e-1 SMART
IG 667 751 1.32e-3 SMART
IG 760 849 7.3e-6 SMART
IGc2 868 941 5.4e-9 SMART
FN3 955 1036 1.01e-11 SMART
transmembrane domain 1078 1100 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123880
Predicted Effect probably damaging
Transcript: ENSMUST00000126297
AA Change: S939I

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: S939I

DomainStartEndE-ValueType
IG 38 132 1.38e-6 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000149086
Meta Mutation Damage Score 0.1566 question?
Coding Region Coverage
  • 1x: 99.5%
  • 3x: 98.4%
  • 10x: 95.6%
  • 20x: 90.2%
Validation Efficiency 90% (36/40)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] 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]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit severe proteinuria associated with kidney defects and die soon after birth. Heterozygotes exhibit fusion of one-third of glomerular foot processes. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akap13 T C 7: 75,327,157 (GRCm39) S719P probably damaging Het
Atxn2l A T 7: 126,096,466 (GRCm39) N425K probably benign Het
B3galt4 G A 17: 34,169,813 (GRCm39) R142C probably damaging Het
Cacna2d2 T C 9: 107,404,249 (GRCm39) probably null Het
Ccar2 A G 14: 70,377,964 (GRCm39) S674P probably damaging Het
Ccm2 T A 11: 6,520,119 (GRCm39) Y56* probably null Het
Cdc14b A T 13: 64,363,490 (GRCm39) V257E probably damaging Het
Cdca8 A C 4: 124,815,798 (GRCm39) S171R probably benign Het
Cep192 C T 18: 67,971,125 (GRCm39) T1042I probably benign Het
Cfap100 T A 6: 90,389,986 (GRCm39) T101S possibly damaging Het
Cfap46 T A 7: 139,222,513 (GRCm39) M1155L probably benign Het
Cyp3a13 T A 5: 137,892,626 (GRCm39) I473F possibly damaging Het
Dclk3 A G 9: 111,298,138 (GRCm39) I561V possibly damaging Het
Dock6 A T 9: 21,744,908 (GRCm39) L556H probably damaging Het
Dqx1 G A 6: 83,038,070 (GRCm39) C486Y probably damaging Het
Drd1 T A 13: 54,207,333 (GRCm39) M294L probably benign Het
Dsel A G 1: 111,788,403 (GRCm39) S711P probably damaging Het
Fcho2 A T 13: 98,869,167 (GRCm39) I568N probably damaging Het
Folr1 A G 7: 101,507,810 (GRCm39) M210T probably damaging Het
Gatc T A 5: 115,478,904 (GRCm39) probably null Het
Gja8 A T 3: 96,826,740 (GRCm39) F307L probably benign Het
H1f7 G A 15: 98,154,636 (GRCm39) T171I unknown Het
Hnrnpd C A 5: 100,114,016 (GRCm39) *87L probably null Het
Hpd C T 5: 123,312,532 (GRCm39) R279H possibly damaging Het
Igfals G A 17: 25,099,457 (GRCm39) V183M probably damaging Het
Izumo1 A G 7: 45,276,598 (GRCm39) Y387C probably benign Het
Kdm5a A G 6: 120,375,999 (GRCm39) N585S probably null Het
Marchf2 C A 17: 33,928,762 (GRCm39) G45C probably damaging Het
Myo15a A T 11: 60,370,442 (GRCm39) R1067S probably benign Het
Naip2 T C 13: 100,298,362 (GRCm39) E558G probably benign Het
Naip2 C T 13: 100,298,368 (GRCm39) G556D probably benign Het
Nell1 A G 7: 49,770,411 (GRCm39) S157G probably damaging Het
Nf1 A T 11: 79,437,859 (GRCm39) E2072D probably damaging Het
Nipal1 CGGG CGG 5: 72,825,334 (GRCm39) probably null Het
Nop2 T A 6: 125,114,149 (GRCm39) V205E probably benign Het
Nudt8 T A 19: 4,051,925 (GRCm39) W179R probably damaging Het
Nutm1 A T 2: 112,080,274 (GRCm39) I547N probably benign Het
Oog2 A C 4: 143,922,856 (GRCm39) T374P probably damaging Het
Or4k5 A T 14: 50,385,384 (GRCm39) F316I probably benign Het
Or8b54 C A 9: 38,686,631 (GRCm39) L27I probably damaging Het
Otud4 T A 8: 80,390,722 (GRCm39) M413K probably benign Het
Pear1 A G 3: 87,667,606 (GRCm39) probably benign Het
Pla2g3 G A 11: 3,438,551 (GRCm39) C67Y probably damaging Het
Plxdc2 A G 2: 16,716,917 (GRCm39) T334A probably benign Het
Ppl G A 16: 4,917,864 (GRCm39) R543W probably damaging Het
Prl5a1 G A 13: 28,333,880 (GRCm39) V128I probably damaging Het
Pth1r A T 9: 110,571,295 (GRCm39) L25Q probably damaging Het
Pth1r T C 9: 110,558,689 (GRCm39) D96G probably benign Het
Rfpl4 G T 7: 5,113,517 (GRCm39) D215E probably damaging Het
Rnf146 T A 10: 29,223,092 (GRCm39) R265* probably null Het
Rpe65 T C 3: 159,312,122 (GRCm39) I207T probably benign Het
Rptn A G 3: 93,305,532 (GRCm39) E955G possibly damaging Het
Rwdd2b A T 16: 87,233,738 (GRCm39) C121S probably damaging Het
Scn10a A G 9: 119,438,340 (GRCm39) I1843T probably damaging Het
Sirt5 A G 13: 43,524,245 (GRCm39) I6V probably benign Het
Slc25a36 A G 9: 96,961,254 (GRCm39) Y261H probably damaging Het
Slc5a3 G A 16: 91,874,383 (GRCm39) A147T probably damaging Het
Stk39 T C 2: 68,240,390 (GRCm39) S114G probably damaging Het
Stxbp1 T C 2: 32,704,979 (GRCm39) probably null Het
Syt3 G T 7: 44,040,106 (GRCm39) G113V probably damaging Het
Tatdn2 A G 6: 113,686,506 (GRCm39) T644A probably damaging Het
Trim9 T A 12: 70,298,791 (GRCm39) probably null Het
Tut1 A G 19: 8,936,719 (GRCm39) N181S probably benign Het
Vill T C 9: 118,895,892 (GRCm39) S151P probably damaging Het
Vmn2r90 A T 17: 17,948,400 (GRCm39) I549F probably damaging Het
Wdfy4 T C 14: 32,801,923 (GRCm39) T1912A possibly damaging Het
Other mutations in Nphs1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00160:Nphs1 APN 7 30,181,976 (GRCm39) missense possibly damaging 0.77
IGL00927:Nphs1 APN 7 30,160,164 (GRCm39) unclassified probably benign
IGL00976:Nphs1 APN 7 30,160,110 (GRCm39) missense possibly damaging 0.78
IGL01397:Nphs1 APN 7 30,186,089 (GRCm39) missense probably benign 0.01
IGL01465:Nphs1 APN 7 30,186,139 (GRCm39) makesense probably null
IGL01889:Nphs1 APN 7 30,159,936 (GRCm39) missense probably damaging 1.00
IGL02383:Nphs1 APN 7 30,181,060 (GRCm39) splice site probably benign
R0020:Nphs1 UTSW 7 30,162,633 (GRCm39) missense probably benign 0.01
R0485:Nphs1 UTSW 7 30,166,940 (GRCm39) missense probably benign
R1115:Nphs1 UTSW 7 30,180,803 (GRCm39) splice site probably benign
R1144:Nphs1 UTSW 7 30,181,103 (GRCm39) splice site probably benign
R1289:Nphs1 UTSW 7 30,170,603 (GRCm39) missense probably damaging 1.00
R1317:Nphs1 UTSW 7 30,181,256 (GRCm39) splice site probably benign
R1617:Nphs1 UTSW 7 30,181,956 (GRCm39) missense probably benign
R1756:Nphs1 UTSW 7 30,160,959 (GRCm39) missense probably benign 0.00
R1937:Nphs1 UTSW 7 30,173,798 (GRCm39) missense probably damaging 1.00
R2144:Nphs1 UTSW 7 30,160,395 (GRCm39) missense probably benign 0.13
R2256:Nphs1 UTSW 7 30,167,417 (GRCm39) missense possibly damaging 0.94
R2257:Nphs1 UTSW 7 30,167,417 (GRCm39) missense possibly damaging 0.94
R2277:Nphs1 UTSW 7 30,166,989 (GRCm39) nonsense probably null
R3104:Nphs1 UTSW 7 30,166,965 (GRCm39) nonsense probably null
R3106:Nphs1 UTSW 7 30,166,965 (GRCm39) nonsense probably null
R3151:Nphs1 UTSW 7 30,159,665 (GRCm39) missense probably benign
R3765:Nphs1 UTSW 7 30,170,635 (GRCm39) missense probably damaging 0.98
R4078:Nphs1 UTSW 7 30,166,945 (GRCm39) nonsense probably null
R4397:Nphs1 UTSW 7 30,181,390 (GRCm39) splice site probably null
R4635:Nphs1 UTSW 7 30,167,432 (GRCm39) missense probably benign 0.39
R4650:Nphs1 UTSW 7 30,181,895 (GRCm39) missense probably benign 0.21
R4811:Nphs1 UTSW 7 30,159,854 (GRCm39) missense probably damaging 1.00
R4850:Nphs1 UTSW 7 30,162,657 (GRCm39) missense possibly damaging 0.78
R5272:Nphs1 UTSW 7 30,181,067 (GRCm39) missense possibly damaging 0.86
R5327:Nphs1 UTSW 7 30,163,250 (GRCm39) missense probably benign 0.00
R5681:Nphs1 UTSW 7 30,186,050 (GRCm39) missense probably benign 0.00
R5865:Nphs1 UTSW 7 30,173,810 (GRCm39) missense probably damaging 1.00
R5975:Nphs1 UTSW 7 30,165,540 (GRCm39) missense possibly damaging 0.82
R6186:Nphs1 UTSW 7 30,165,059 (GRCm39) missense probably damaging 0.98
R6198:Nphs1 UTSW 7 30,167,340 (GRCm39) missense probably damaging 0.97
R6353:Nphs1 UTSW 7 30,173,969 (GRCm39) missense probably damaging 0.99
R7405:Nphs1 UTSW 7 30,162,253 (GRCm39) missense possibly damaging 0.46
R7647:Nphs1 UTSW 7 30,181,390 (GRCm39) splice site probably null
R7767:Nphs1 UTSW 7 30,162,733 (GRCm39) missense probably damaging 1.00
R8132:Nphs1 UTSW 7 30,181,478 (GRCm39) missense probably benign 0.02
R8485:Nphs1 UTSW 7 30,165,598 (GRCm39) missense probably damaging 0.98
R8678:Nphs1 UTSW 7 30,163,284 (GRCm39) missense probably damaging 1.00
R8890:Nphs1 UTSW 7 30,162,080 (GRCm39) missense probably damaging 1.00
R8946:Nphs1 UTSW 7 30,162,625 (GRCm39) missense probably damaging 1.00
R9133:Nphs1 UTSW 7 30,160,092 (GRCm39) nonsense probably null
R9159:Nphs1 UTSW 7 30,165,026 (GRCm39) missense possibly damaging 0.93
R9347:Nphs1 UTSW 7 30,170,594 (GRCm39) missense probably damaging 1.00
R9547:Nphs1 UTSW 7 30,180,875 (GRCm39) missense probably benign 0.00
R9548:Nphs1 UTSW 7 30,180,875 (GRCm39) missense probably benign 0.00
R9607:Nphs1 UTSW 7 30,163,012 (GRCm39) missense probably damaging 1.00
R9626:Nphs1 UTSW 7 30,166,991 (GRCm39) missense probably benign 0.16
R9720:Nphs1 UTSW 7 30,165,499 (GRCm39) missense possibly damaging 0.83
R9733:Nphs1 UTSW 7 30,166,955 (GRCm39) missense probably damaging 1.00
X0028:Nphs1 UTSW 7 30,166,929 (GRCm39) missense probably null 0.01
Z1177:Nphs1 UTSW 7 30,170,328 (GRCm39) missense probably damaging 1.00
Z1186:Nphs1 UTSW 7 30,159,775 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GAACTGCTCATGTGCCAGATACCC -3'
(R):5'- CATACCTGCATGGCGAGAACAGTC -3'

Sequencing Primer
(F):5'- cagatacccacaggttgtgag -3'
(R):5'- TGGCGAGAACAGTCAGCTC -3'
Posted On 2014-01-09