Incidental Mutation 'R8132:Nphs1'
ID 632072
Institutional Source Beutler Lab
Gene Symbol Nphs1
Ensembl Gene ENSMUSG00000006649
Gene Name nephrosis 1, nephrin
Synonyms nephrin
MMRRC Submission 067895-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8132 (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 G at 30181478 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 1169 (E1169G)
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: E1169G

PolyPhen 2 Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: E1169G

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: E1155G

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: E1155G

DomainStartEndE-ValueType
IG 38 132 1.38e-6 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000149086
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.6%
  • 10x: 98.6%
  • 20x: 94.2%
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb10 C T 8: 124,691,757 (GRCm39) A403T Het
Abhd16b G A 2: 181,135,760 (GRCm39) A221T probably damaging Het
Arhgef1 C T 7: 24,607,087 (GRCm39) probably benign Het
Arhgef1 C T 7: 24,619,174 (GRCm39) Q472* probably null Het
Calr3 C T 8: 73,181,023 (GRCm39) G298S probably damaging Het
Chrng A G 1: 87,133,718 (GRCm39) T15A unknown Het
CK137956 T A 4: 127,845,075 (GRCm39) K223* probably null Het
Clca3b A T 3: 144,552,935 (GRCm39) S97T probably benign Het
Cops7b G T 1: 86,514,916 (GRCm39) G102V probably damaging Het
Dennd1a T A 2: 37,748,072 (GRCm39) S382C probably damaging Het
Fdps G A 3: 89,006,693 (GRCm39) Q66* probably null Het
Gemin4 T C 11: 76,103,739 (GRCm39) T341A probably benign Het
Grk3 A G 5: 113,109,355 (GRCm39) S201P unknown Het
Hgf C T 5: 16,807,329 (GRCm39) T407I probably damaging Het
Hip1r C T 5: 124,135,290 (GRCm39) R446C probably damaging Het
Hyal6 A T 6: 24,740,827 (GRCm39) I327L possibly damaging Het
Ifna15 T C 4: 88,475,920 (GRCm39) E188G possibly damaging Het
Igip A G 18: 36,434,266 (GRCm39) S11G probably benign Het
Igkv5-39 A G 6: 69,877,589 (GRCm39) Y56H probably damaging Het
Jph1 G A 1: 17,086,379 (GRCm39) T381I probably damaging Het
Lrrc55 T C 2: 85,022,259 (GRCm39) I311V probably benign Het
Mrps35 T A 6: 146,949,661 (GRCm39) D58E probably benign Het
Ms4a4d C A 19: 11,535,310 (GRCm39) P203T probably benign Het
Naip1 T G 13: 100,573,883 (GRCm39) E225D possibly damaging Het
Ncapg2 T A 12: 116,407,967 (GRCm39) I989N possibly damaging Het
Nek3 A T 8: 22,647,036 (GRCm39) Y166* probably null Het
Nudt15 G A 14: 73,759,099 (GRCm39) P123L probably benign Het
Or10c1 T A 17: 37,522,207 (GRCm39) E179V probably damaging Het
Or10q1b G A 19: 13,682,584 (GRCm39) C131Y probably damaging Het
Or5ac22 T C 16: 59,134,907 (GRCm39) I288V possibly damaging Het
Or6k14 T A 1: 173,927,737 (GRCm39) S238T probably damaging Het
Or8a1b C T 9: 37,623,369 (GRCm39) V69M probably benign Het
Pcdha5 T C 18: 37,093,694 (GRCm39) S68P possibly damaging Het
Plec G T 15: 76,074,773 (GRCm39) A330E unknown Het
Rpa3 A C 6: 8,256,790 (GRCm39) I63S probably damaging Het
Rsf1 CG CGACGGCGGGG 7: 97,229,115 (GRCm39) probably benign Het
Snap25 A T 2: 136,611,748 (GRCm39) K83N probably benign Het
Sos1 T G 17: 80,716,031 (GRCm39) Q977P probably damaging Het
Spag16 A G 1: 70,420,461 (GRCm39) Y483C probably damaging Het
Speg A G 1: 75,399,639 (GRCm39) E2362G probably damaging Het
Swap70 A G 7: 109,855,084 (GRCm39) D128G probably damaging Het
Syngap1 G A 17: 27,177,154 (GRCm39) M545I probably damaging Het
Tdpoz6 G A 3: 93,599,452 (GRCm39) Q306* probably null Het
Tmem147 T C 7: 30,427,872 (GRCm39) E110G probably damaging Het
Tmem156 T A 5: 65,233,098 (GRCm39) I155F probably benign Het
Trim25 C A 11: 88,907,432 (GRCm39) A597E probably damaging Het
Ttc7b T C 12: 100,413,131 (GRCm39) Y229C probably damaging Het
Utrn T A 10: 12,558,154 (GRCm39) Q1435L probably damaging Het
Zbtb41 T C 1: 139,350,955 (GRCm39) S23P probably benign Het
Zeb2 T A 2: 44,879,142 (GRCm39) I1075F probably 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
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
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'- TAATCACTGCCATCTCCTGGG -3'
(R):5'- CAATACCTGTGAAGGCTGGAG -3'

Sequencing Primer
(F):5'- ATCTCCTGGGACCTGAGAGTCAAG -3'
(R):5'- TGTCTGCCGTGATAAGAGCAACTC -3'
Posted On 2020-06-30