Incidental Mutation 'R5865:Nphs1'
ID 454121
Institutional Source Beutler Lab
Gene Symbol Nphs1
Ensembl Gene ENSMUSG00000006649
Gene Name nephrosis 1, nephrin
Synonyms nephrin
MMRRC Submission 044074-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5865 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 30157740-30186648 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 30173810 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 989 (I989N)
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: I989N

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: I989N

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: I975N

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: I975N

DomainStartEndE-ValueType
IG 38 132 1.38e-6 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000149086
Meta Mutation Damage Score 0.9239 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.4%
  • 10x: 96.7%
  • 20x: 88.7%
Validation Efficiency 91% (59/65)
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: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actl6a G A 3: 32,766,277 (GRCm39) V48M possibly damaging Het
Adamts2 T G 11: 50,694,781 (GRCm39) Y1189* probably null Het
Bpifb9a T C 2: 154,108,756 (GRCm39) I419T probably benign Het
Ccbe1 A T 18: 66,216,222 (GRCm39) I167N possibly damaging Het
Ccdc187 T C 2: 26,183,380 (GRCm39) T207A probably benign Het
Cd300lf G A 11: 115,017,126 (GRCm39) L66F probably damaging Het
Cenpk A G 13: 104,372,702 (GRCm39) *92W probably null Het
Col12a1 A T 9: 79,511,760 (GRCm39) S2950R probably benign Het
Dnah3 T C 7: 119,574,331 (GRCm39) T2154A probably benign Het
Ebna1bp2 A T 4: 118,478,332 (GRCm39) probably benign Het
Elac2 G T 11: 64,888,783 (GRCm39) C532F probably benign Het
Fam171a1 T A 2: 3,226,374 (GRCm39) D377E probably benign Het
Haus6 A G 4: 86,504,594 (GRCm39) C466R possibly damaging Het
Il4ra T C 7: 125,174,348 (GRCm39) S297P probably benign Het
Itgb4 C T 11: 115,881,748 (GRCm39) R766W probably damaging Het
Kank4 T C 4: 98,659,630 (GRCm39) Y816C possibly damaging Het
Kcnc4 A T 3: 107,365,515 (GRCm39) probably null Het
Kif21b C T 1: 136,078,875 (GRCm39) R408* probably null Het
Lrrc31 A G 3: 30,733,289 (GRCm39) V475A probably benign Het
Map2k1 C T 9: 64,098,548 (GRCm39) probably null Het
Mc3r T A 2: 172,091,592 (GRCm39) N271K possibly damaging Het
Ms4a14 A G 19: 11,281,581 (GRCm39) S326P possibly damaging Het
Muc6 T A 7: 141,236,769 (GRCm39) I358F probably damaging Het
Myo5c A G 9: 75,204,770 (GRCm39) D1541G probably damaging Het
Myof T C 19: 37,899,382 (GRCm39) S1793G probably damaging Het
Nfkb1 T A 3: 135,309,541 (GRCm39) T518S probably damaging Het
Or5m12 T C 2: 85,734,865 (GRCm39) T178A probably benign Het
Pcdha5 T C 18: 37,094,474 (GRCm39) F328L probably benign Het
Pclo T A 5: 14,764,492 (GRCm39) S4322T probably benign Het
Peg10 A G 6: 4,754,375 (GRCm39) N52S probably damaging Het
Phf10 A C 17: 15,175,272 (GRCm39) probably benign Het
Pip4p1 A G 14: 51,166,332 (GRCm39) probably benign Het
Psme4 T C 11: 30,741,993 (GRCm39) I152T possibly damaging Het
Ptpn18 T A 1: 34,510,644 (GRCm39) probably benign Het
Rufy4 A T 1: 74,185,914 (GRCm39) Y527F probably damaging Het
Snx32 T C 19: 5,546,382 (GRCm39) M293V probably benign Het
Sorl1 A T 9: 41,894,330 (GRCm39) L1827M possibly damaging Het
Sstr5 T A 17: 25,710,218 (GRCm39) D337V probably benign Het
Tcaf3 A G 6: 42,573,631 (GRCm39) F194L probably benign Het
Tcerg1 T A 18: 42,669,413 (GRCm39) W459R probably damaging Het
Tet2 T A 3: 133,192,860 (GRCm39) I525L probably benign Het
Trim43b C T 9: 88,967,659 (GRCm39) V325I probably benign Het
Txndc11 A T 16: 10,940,552 (GRCm39) I180K probably damaging Het
Vmn1r193 A G 13: 22,403,395 (GRCm39) L199P probably damaging Het
Vmn2r110 A G 17: 20,804,557 (GRCm39) M121T probably benign Het
Zfhx4 G C 3: 5,467,719 (GRCm39) A2626P probably damaging Het
Zfp445 C T 9: 122,682,552 (GRCm39) S463N probably benign Het
Zwilch T A 9: 64,080,190 (GRCm39) probably null 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
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'- GCCACTGTGAATAGAGAGAACC -3'
(R):5'- CCTGTACCGTGTAGAAGGCTTC -3'

Sequencing Primer
(F):5'- TGTTCTCAGGAGACTCCGACAG -3'
(R):5'- TTCAGCCCAGTCAGTGTGAAG -3'
Posted On 2017-02-10