Incidental Mutation 'R9548:Nphs1'
ID 720238
Institutional Source Beutler Lab
Gene Symbol Nphs1
Ensembl Gene ENSMUSG00000006649
Gene Name nephrosis 1, nephrin
Synonyms nephrin
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9548 (G1)
Quality Score 225.009
Status Not validated
Chromosome 7
Chromosomal Location 30157740-30186648 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 30180875 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Phenylalanine at position 1093 (S1093F)
Ref Sequence ENSEMBL: ENSMUSP00000006825 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006825] [ENSMUST00000126297]
AlphaFold Q9QZS7
Predicted Effect probably benign
Transcript: ENSMUST00000006825
AA Change: S1093F

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: S1093F

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 probably benign
Transcript: ENSMUST00000126297
AA Change: S1079F

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: S1079F

DomainStartEndE-ValueType
IG 38 132 1.38e-6 SMART
Predicted Effect unknown
Transcript: ENSMUST00000149086
AA Change: P61S
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.3%
  • 20x: 97.5%
Validation Efficiency
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
Ankfy1 G A 11: 72,641,005 (GRCm39) probably null Het
Arid1b A G 17: 5,385,262 (GRCm39) Y1340C probably damaging Het
Bcl2 C A 1: 106,640,508 (GRCm39) A35S probably benign Het
Brf2 A T 8: 27,614,623 (GRCm39) S188T probably benign Het
Carmil1 C A 13: 24,460,516 (GRCm39) G21V probably damaging Het
Cavin4 T C 4: 48,663,956 (GRCm39) V112A probably benign Het
Cd300lf T C 11: 115,007,858 (GRCm39) E319G probably benign Het
Cd44 A T 2: 102,661,832 (GRCm39) D587E possibly damaging Het
Cfap53 A T 18: 74,438,040 (GRCm39) T239S possibly damaging Het
Cma2 A C 14: 56,211,256 (GRCm39) I239L probably damaging Het
Cnot1 A T 8: 96,482,854 (GRCm39) M733K probably benign Het
Cyp2f2 A G 7: 26,829,170 (GRCm39) D225G probably benign Het
Cyp4f40 G A 17: 32,890,158 (GRCm39) R276H probably benign Het
Cytip A T 2: 58,041,141 (GRCm39) F88L probably damaging Het
Dnaaf2 T C 12: 69,244,776 (GRCm39) N95S probably damaging Het
Dnah5 C A 15: 28,328,025 (GRCm39) T2133K possibly damaging Het
Dusp9 TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG X: 72,684,217 (GRCm39) probably benign Het
Elapor2 G A 5: 9,490,859 (GRCm39) G623D probably damaging Het
Epn2 A T 11: 61,436,988 (GRCm39) S195T probably benign Het
Exoc3 A T 13: 74,330,285 (GRCm39) Y521N possibly damaging Het
Fbxo10 C A 4: 45,058,970 (GRCm39) V256L probably damaging Het
Fis1 A T 5: 136,991,907 (GRCm39) T34S probably benign Het
Gm10309 A T 17: 86,806,161 (GRCm39) C118S unknown Het
Grip1 G A 10: 119,874,569 (GRCm39) E778K possibly damaging Het
Hook1 T A 4: 95,891,808 (GRCm39) V340E probably damaging Het
Ifng C A 10: 118,277,128 (GRCm39) H23Q probably benign Het
Lect2 C T 13: 56,694,660 (GRCm39) E32K probably benign Het
Lrp1 T G 10: 127,388,733 (GRCm39) T3239P probably damaging Het
Lrrc14b T A 13: 74,511,996 (GRCm39) Y28F probably benign Het
Maml3 A T 3: 51,763,791 (GRCm39) V391E possibly damaging Het
Map3k8 C T 18: 4,349,141 (GRCm39) R59H probably benign Het
Med1 G T 11: 98,070,884 (GRCm39) L120I possibly damaging Het
Muc5b C A 7: 141,421,648 (GRCm39) H4349N possibly damaging Het
Myo1h C T 5: 114,499,154 (GRCm39) P110S probably benign Het
Nol10 T G 12: 17,466,144 (GRCm39) I513S possibly damaging Het
Or12e10 A T 2: 87,641,097 (GRCm39) N311I probably damaging Het
Or4b1b T C 2: 90,111,991 (GRCm39) *309W probably null Het
Or56b1b A T 7: 108,164,334 (GRCm39) S223T possibly damaging Het
Or5p72 A T 7: 108,022,416 (GRCm39) T213S possibly damaging Het
Or5w8 A T 2: 87,688,040 (GRCm39) I174F probably damaging Het
Pcdh17 A T 14: 84,685,402 (GRCm39) Y623F possibly damaging Het
Pdzd8 T A 19: 59,289,826 (GRCm39) I525F probably benign Het
Peak1 G T 9: 56,113,917 (GRCm39) Q1675K probably benign Het
Perm1 T C 4: 156,302,290 (GRCm39) V278A probably benign Het
Ppp2r5d G A 17: 46,998,527 (GRCm39) R115C probably damaging Het
Rnf169 A T 7: 99,574,690 (GRCm39) L635Q probably damaging Het
Sacs A G 14: 61,440,692 (GRCm39) T913A probably benign Het
Sh3bp1 A T 15: 78,788,673 (GRCm39) I233F possibly damaging Het
Skint9 T G 4: 112,276,346 (GRCm39) L8F probably benign Het
Slc1a4 A T 11: 20,258,041 (GRCm39) N360K probably damaging Het
Slc22a16 T A 10: 40,460,865 (GRCm39) Y243* probably null Het
Slc22a19 C A 19: 7,659,219 (GRCm39) probably null Het
Smarcal1 T C 1: 72,671,999 (GRCm39) I840T possibly damaging Het
Spata13 A G 14: 60,991,303 (GRCm39) K1019E possibly damaging Het
Steap1 A G 5: 5,790,700 (GRCm39) S83P possibly damaging Het
Synj2bp T C 12: 81,551,382 (GRCm39) H78R probably damaging Het
Tcstv7a T A 13: 120,289,924 (GRCm39) I91F probably benign Het
Tjp3 T C 10: 81,113,833 (GRCm39) E475G probably damaging Het
Top3a A G 11: 60,644,768 (GRCm39) V312A probably benign Het
Traip C A 9: 107,833,099 (GRCm39) T45N probably damaging Het
Ttn T C 2: 76,573,691 (GRCm39) Y25734C probably damaging Het
Unc79 T A 12: 102,977,495 (GRCm39) V166D probably damaging Het
Urgcp C A 11: 5,667,622 (GRCm39) V282F possibly damaging Het
Vmn1r184 G A 7: 25,966,734 (GRCm39) S160N probably benign Het
Wdfy3 T C 5: 102,033,059 (GRCm39) D2231G probably damaging Het
Zan C T 5: 137,401,323 (GRCm39) G4132D unknown 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
R1024:Nphs1 UTSW 7 30,173,702 (GRCm39) missense probably damaging 1.00
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
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'- CAAGTGTCCTAGGCGATTTGG -3'
(R):5'- TCTGAGATCTCTGGGAGAAACGAG -3'

Sequencing Primer
(F):5'- CGTCAGGTTGGCACTGAAGAC -3'
(R):5'- CAGCTTGGCACTGAGAAA -3'
Posted On 2022-07-18