Incidental Mutation 'R9159:Nphs1'
ID 695575
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 # R9159 (G1)
Quality Score 225.009
Status Validated
Chromosome 7
Chromosomal Location 30157740-30186648 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 30165026 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Valine at position 540 (F540V)
Ref Sequence ENSEMBL: ENSMUSP00000006825 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006825] [ENSMUST00000126297]
AlphaFold Q9QZS7
Predicted Effect possibly damaging
Transcript: ENSMUST00000006825
AA Change: F540V

PolyPhen 2 Score 0.929 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: F540V

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 possibly damaging
Transcript: ENSMUST00000126297
AA Change: F526V

PolyPhen 2 Score 0.913 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: F526V

DomainStartEndE-ValueType
IG 38 132 1.38e-6 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.2%
Validation Efficiency 97% (72/74)
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: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9930012K11Rik A T 14: 70,394,238 (GRCm39) M179K probably benign Het
A030003K21Rik A G 1: 82,920,787 (GRCm39) V86A unknown Het
AC133488.1 A T 16: 18,440,075 (GRCm39) V363E probably benign Het
Adamts16 A G 13: 70,901,408 (GRCm39) S890P probably benign Het
Adgrf4 A G 17: 42,973,293 (GRCm39) V685A probably benign Het
Aff1 T A 5: 103,990,131 (GRCm39) M867K possibly damaging Het
Apba3 T A 10: 81,106,867 (GRCm39) S225T Het
Aplp1 T A 7: 30,141,775 (GRCm39) T228S probably benign Het
Arhgap18 A G 10: 26,730,886 (GRCm39) D188G probably benign Het
BC024063 T A 10: 81,944,906 (GRCm39) S175R possibly damaging Het
Bloc1s6 T G 2: 122,580,548 (GRCm39) S2R probably damaging Het
Cd209b A G 8: 3,974,245 (GRCm39) I119T possibly damaging Het
Cdk8 T C 5: 146,168,549 (GRCm39) V16A probably damaging Het
Cep295 A G 9: 15,252,904 (GRCm39) M308T probably benign Het
Cfap53 T A 18: 74,416,272 (GRCm39) Y2N probably damaging Het
Col28a1 T A 6: 8,014,993 (GRCm39) D804V probably damaging Het
Csta3 G A 16: 36,038,069 (GRCm39) V69I probably benign Het
Cyp2c40 A T 19: 39,762,317 (GRCm39) D443E probably damaging Het
Cyp2d9 A G 15: 82,338,572 (GRCm39) D202G possibly damaging Het
Dchs1 G A 7: 105,415,126 (GRCm39) A686V probably benign Het
Egf A T 3: 129,472,026 (GRCm39) N1199K probably benign Het
Eva1a A G 6: 82,068,855 (GRCm39) R61G possibly damaging Het
Exoc6 T A 19: 37,597,478 (GRCm39) D626E probably benign Het
Exosc10 T C 4: 148,663,916 (GRCm39) probably null Het
Firrm A G 1: 163,814,514 (GRCm39) I143T probably damaging Het
Gm12888 T C 4: 121,176,600 (GRCm39) Q67R probably null Het
Gm16485 A G 9: 8,972,319 (GRCm39) S62G unknown Het
Gng4 T C 13: 13,999,896 (GRCm39) I55T probably damaging Het
Gpihbp1 A G 15: 75,469,830 (GRCm39) S182G possibly damaging Het
Hax1 T C 3: 89,903,127 (GRCm39) R251G probably damaging Het
Igf2bp2 G A 16: 21,900,502 (GRCm39) T213I probably damaging Het
Il23a T A 10: 128,133,427 (GRCm39) K66* probably null Het
Itga2 A T 13: 115,014,298 (GRCm39) L210* probably null Het
Ltbp2 G A 12: 84,837,864 (GRCm39) P1192L probably benign Het
Matr3 T A 18: 35,712,355 (GRCm39) M389K possibly damaging Het
Mettl15 T C 2: 108,923,444 (GRCm39) D326G probably damaging Het
Mta1 T A 12: 113,100,025 (GRCm39) V645E probably damaging Het
Muc5ac T C 7: 141,363,529 (GRCm39) I2280T unknown Het
Naa15 T A 3: 51,358,802 (GRCm39) N362K probably benign Het
Necab2 T C 8: 120,189,303 (GRCm39) Y158H probably damaging Het
Nphp3 T A 9: 103,897,980 (GRCm39) L523Q probably damaging Het
Or2av9 A G 11: 58,381,350 (GRCm39) V77A probably damaging Het
Or2k2 A G 4: 58,785,320 (GRCm39) I134T probably benign Het
Or5p55 A T 7: 107,567,524 (GRCm39) R307* probably null Het
Ppa1 A T 10: 61,496,784 (GRCm39) I91F probably damaging Het
Prdm6 C A 18: 53,598,019 (GRCm39) A127D unknown Het
Prdm8 T C 5: 98,334,175 (GRCm39) F581L probably damaging Het
Rbbp6 T C 7: 122,589,428 (GRCm39) I372T probably damaging Het
Rnf144b A G 13: 47,396,348 (GRCm39) I228M probably damaging Het
Rsf1 CG CGACGGCGGGG 7: 97,229,115 (GRCm39) probably benign Het
Setd2 T C 9: 110,374,385 (GRCm39) probably null Het
Sez6l T C 5: 112,613,824 (GRCm39) H441R possibly damaging Het
Shbg G A 11: 69,506,430 (GRCm39) L327F probably benign Het
Sik3 C T 9: 46,123,539 (GRCm39) Q1113* probably null Het
Smad2 T A 18: 76,395,573 (GRCm39) I4N possibly damaging Het
Spata31h1 G A 10: 82,118,524 (GRCm39) R4829* probably null Het
Sult2b1 T A 7: 45,391,534 (GRCm39) E84V probably damaging Het
Tbc1d8 A G 1: 39,444,474 (GRCm39) Y162H Het
Tedc2 A G 17: 24,436,705 (GRCm39) L308P probably damaging Het
Tmc5 T C 7: 118,233,264 (GRCm39) V26A probably benign Het
Tmem120b T A 5: 123,242,566 (GRCm39) N181K possibly damaging Het
Tmem229b T G 12: 79,011,448 (GRCm39) N161T possibly damaging Het
Tmem43 A C 6: 91,459,291 (GRCm39) D254A probably benign Het
Trpv6 T C 6: 41,603,074 (GRCm39) D266G probably benign Het
Tspan9 A G 6: 127,943,717 (GRCm39) I102T possibly damaging Het
Ung A G 5: 114,270,166 (GRCm39) probably benign Het
Upp2 C T 2: 58,667,996 (GRCm39) H230Y probably damaging Het
Vmn1r184 G A 7: 25,966,545 (GRCm39) S97N possibly damaging Het
Vmn2r73 A T 7: 85,521,931 (GRCm39) V136E possibly damaging Het
Wdr20rt T C 12: 65,272,918 (GRCm39) V127A probably damaging Het
Yme1l1 T A 2: 23,063,058 (GRCm39) F210I probably damaging Het
Yrdc T C 4: 124,747,811 (GRCm39) probably null Het
Zfhx4 G T 3: 5,464,312 (GRCm39) R1515L probably damaging Het
Zfhx4 C T 3: 5,466,217 (GRCm39) P2150L probably damaging Het
Zfp267 C A 3: 36,219,902 (GRCm39) H642N possibly damaging Het
Zfp988 C T 4: 147,416,450 (GRCm39) P295S 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
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
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'- TCACACAAAGGCCCTCTCTG -3'
(R):5'- AGGTCAAGTTCAAGGCGTC -3'

Sequencing Primer
(F):5'- CCTCTCTGGGCTAACGGC -3'
(R):5'- ACGAGTTGGCCAGGATGGTC -3'
Posted On 2022-01-20