Incidental Mutation 'R9607:Nphs1'
ID 723936
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 # R9607 (G1)
Quality Score 225.009
Status Not validated
Chromosome 7
Chromosomal Location 30157740-30186648 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 30163012 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 430 (T430S)
Ref Sequence ENSEMBL: ENSMUSP00000006825 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006825] [ENSMUST00000126297]
AlphaFold Q9QZS7
Predicted Effect probably damaging
Transcript: ENSMUST00000006825
AA Change: T430S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: T430S

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 damaging
Transcript: ENSMUST00000126297
AA Change: T416S

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: T416S

DomainStartEndE-ValueType
IG 38 132 1.38e-6 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aak1 T C 6: 86,914,068 (GRCm39) probably null Het
Atp8a1 T C 5: 67,817,250 (GRCm39) Y927C Het
Bckdhb A G 9: 83,871,344 (GRCm39) I208V probably benign Het
Cacna1g T C 11: 94,356,714 (GRCm39) I141V probably benign Het
Celsr1 A G 15: 85,915,229 (GRCm39) S915P Het
Celsr3 G A 9: 108,717,701 (GRCm39) probably null Het
Cep295 A T 9: 15,234,009 (GRCm39) D2262E probably damaging Het
Chil3 T C 3: 106,067,685 (GRCm39) K160R probably null Het
Cmtr1 G T 17: 29,893,196 (GRCm39) A72S probably benign Het
Cpa5 T C 6: 30,626,338 (GRCm39) F233S probably damaging Het
Creb3l3 G A 10: 80,920,735 (GRCm39) R432W probably damaging Het
Csdc2 A G 15: 81,831,088 (GRCm39) D45G possibly damaging Het
Csmd3 G T 15: 47,618,811 (GRCm39) T1859K probably damaging Het
Cxxc1 T C 18: 74,353,479 (GRCm39) probably null Het
Dcc A G 18: 71,721,072 (GRCm39) S430P probably damaging Het
Dera T G 6: 137,833,732 (GRCm39) S270A unknown Het
Dnaaf1 A G 8: 120,309,350 (GRCm39) E146G possibly damaging Het
Dsg4 A T 18: 20,586,047 (GRCm39) T246S probably benign Het
Eif4g3 A G 4: 137,893,045 (GRCm39) E766G probably benign Het
Ep400 A C 5: 110,831,805 (GRCm39) C2146G unknown Het
Epas1 A T 17: 87,134,038 (GRCm39) T516S probably benign Het
Espn A G 4: 152,219,939 (GRCm39) S395P probably benign Het
Fam124b T A 1: 80,190,813 (GRCm39) Q190L probably damaging Het
Filip1 T A 9: 79,726,402 (GRCm39) D739V probably damaging Het
Flg2 A G 3: 93,108,719 (GRCm39) Y249C probably damaging Het
Gon4l T A 3: 88,765,751 (GRCm39) S391T probably damaging Het
Hoxa5 G T 6: 52,181,196 (GRCm39) Y45* probably null Het
Ift172 A G 5: 31,410,913 (GRCm39) F1715S Het
Klhdc9 T A 1: 171,187,124 (GRCm39) H262L probably damaging Het
Krt16 C A 11: 100,138,453 (GRCm39) D232Y probably damaging Het
Lrrd1 A G 5: 3,901,561 (GRCm39) E622G probably damaging Het
Mars1 A T 10: 127,144,493 (GRCm39) C182* probably null Het
Mcm5 C T 8: 75,844,168 (GRCm39) S313F probably benign Het
Msrb2 C A 2: 19,399,130 (GRCm39) N164K probably damaging Het
Mtcl2 T G 2: 156,869,488 (GRCm39) E1049A probably damaging Het
Muc2 T A 7: 141,305,190 (GRCm39) C604S Het
Mup17 T C 4: 61,511,903 (GRCm39) I124V probably benign Het
Myo18b T C 5: 113,022,544 (GRCm39) M283V unknown Het
Ndn C T 7: 61,998,337 (GRCm39) P61L possibly damaging Het
Nepro T C 16: 44,551,832 (GRCm39) L230P probably damaging Het
Nes A G 3: 87,883,513 (GRCm39) N591D probably benign Het
Nfrkb T C 9: 31,326,066 (GRCm39) S1170P possibly damaging Het
Nrp1 T C 8: 129,152,262 (GRCm39) V157A probably benign Het
Nup188 T A 2: 30,197,724 (GRCm39) D259E probably benign Het
Or52n5 T C 7: 104,588,207 (GRCm39) M158T probably benign Het
Or5b109 A T 19: 13,211,953 (GRCm39) N113I Het
Or8b1c A G 9: 38,384,913 (GRCm39) Y290C probably damaging Het
Or9s18 G T 13: 65,300,885 (GRCm39) M282I probably benign Het
Pcdha8 T A 18: 37,126,217 (GRCm39) L233Q probably damaging Het
Pcdhga12 T A 18: 37,901,389 (GRCm39) F740L probably damaging Het
Pglyrp4 G A 3: 90,638,151 (GRCm39) G155D probably damaging Het
Piezo2 G A 18: 63,519,347 (GRCm39) probably benign Het
Pirb G A 7: 3,720,617 (GRCm39) R294C possibly damaging Het
Ppil1 A T 17: 29,470,481 (GRCm39) *167K probably null Het
Prdm10 G T 9: 31,260,486 (GRCm39) D647Y probably damaging Het
Prkn A G 17: 12,222,963 (GRCm39) Y371C probably damaging Het
Prrc2b T A 2: 32,098,794 (GRCm39) I702N probably damaging Het
Rnf26rt A T 6: 76,473,923 (GRCm39) L231* probably null Het
Rtp4 T A 16: 23,339,226 (GRCm39) probably null Het
Sema6c A G 3: 95,076,545 (GRCm39) H277R probably benign Het
Slc14a1 C A 18: 78,152,807 (GRCm39) A367S probably damaging Het
Slc41a2 A G 10: 83,119,631 (GRCm39) L377P probably damaging Het
Svil T C 18: 5,058,126 (GRCm39) Y630H possibly damaging Het
Tbata A G 10: 61,011,626 (GRCm39) H54R probably benign Het
Tnfaip2 C A 12: 111,412,069 (GRCm39) Q157K possibly damaging Het
Trappc14 T C 5: 138,259,862 (GRCm39) D398G probably damaging Het
Ttn C T 2: 76,715,357 (GRCm39) E7912K unknown Het
Vmn2r74 T A 7: 85,610,619 (GRCm39) R24S probably benign Het
Vmn2r90 G A 17: 17,953,638 (GRCm39) V601M possibly damaging Het
Vmn2r-ps117 A G 17: 19,043,940 (GRCm39) T339A probably benign Het
Xirp2 C T 2: 67,341,106 (GRCm39) H1116Y possibly damaging Het
Xrcc1 A G 7: 24,265,690 (GRCm39) D156G probably benign 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
R9548:Nphs1 UTSW 7 30,180,875 (GRCm39) missense probably benign 0.00
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'- CAGTTCCTGGGTCTTATAGAGG -3'
(R):5'- TCAATCCACAGCTTCTGGGC -3'

Sequencing Primer
(F):5'- GATGGGAAAGTTTCATGTGTCC -3'
(R):5'- GATGGTGAAGAGACACATTTACATC -3'
Posted On 2022-09-12