Incidental Mutation 'R5975:Nphs1'
ID 471682
Institutional Source Beutler Lab
Gene Symbol Nphs1
Ensembl Gene ENSMUSG00000006649
Gene Name nephrosis 1, nephrin
Synonyms nephrin
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5975 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 30157740-30186648 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 30165540 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 636 (T636S)
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: T636S

PolyPhen 2 Score 0.821 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: T636S

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: T622S

PolyPhen 2 Score 0.427 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: T622S

DomainStartEndE-ValueType
IG 38 132 1.38e-6 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152625
Meta Mutation Damage Score 0.1833 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.8%
  • 20x: 93.3%
Validation Efficiency 98% (80/82)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9430038I01Rik T C 7: 136,989,021 (GRCm39) probably benign Het
Abhd14a A T 9: 106,321,150 (GRCm39) probably null Het
Actn2 T C 13: 12,355,378 (GRCm39) N2D probably benign Het
Adcy9 T C 16: 4,129,431 (GRCm39) E722G probably damaging Het
Alox12 C A 11: 70,133,609 (GRCm39) V572L possibly damaging Het
Ankrd11 T C 8: 123,616,488 (GRCm39) I2434V possibly damaging Het
Anks1 T A 17: 28,210,421 (GRCm39) probably null Het
Bltp1 C T 3: 37,023,370 (GRCm39) T2233I possibly damaging Het
Bpifa3 T A 2: 153,978,241 (GRCm39) S148T probably damaging Het
Bptf C T 11: 106,926,690 (GRCm39) probably benign Het
Cabin1 A T 10: 75,493,673 (GRCm39) L1655H probably damaging Het
Ccdc13 G T 9: 121,656,301 (GRCm39) Q171K probably benign Het
Ccdc33 T A 9: 58,024,761 (GRCm39) Q155L possibly damaging Het
Cckbr G A 7: 105,119,826 (GRCm39) G280E probably benign Het
Cdk11b G A 4: 155,732,697 (GRCm39) probably benign Het
Celsr1 G T 15: 85,803,239 (GRCm39) probably null Het
Cenpj A T 14: 56,801,523 (GRCm39) I150N possibly damaging Het
Cep135 C A 5: 76,788,737 (GRCm39) A1110E possibly damaging Het
Chit1 C A 1: 134,074,364 (GRCm39) H224N probably damaging Het
Cul5 T C 9: 53,534,093 (GRCm39) R680G probably damaging Het
Dhx58 C A 11: 100,593,035 (GRCm39) R224L probably damaging Het
Dlx1 C A 2: 71,361,353 (GRCm39) N122K probably damaging Het
Dnah5 A C 15: 28,234,428 (GRCm39) D279A probably damaging Het
Dnai4 G A 4: 102,906,786 (GRCm39) P676S probably benign Het
Efcab3 A G 11: 104,578,375 (GRCm39) probably benign Het
Enpp3 A G 10: 24,650,740 (GRCm39) W799R probably benign Het
Ercc5 A G 1: 44,212,566 (GRCm39) T675A probably benign Het
Farsa T A 8: 85,591,061 (GRCm39) probably null Het
Fbxw15 A T 9: 109,384,320 (GRCm39) V397D probably damaging Het
Fcrl5 G A 3: 87,349,410 (GRCm39) V62I probably benign Het
Gart A G 16: 91,421,224 (GRCm39) S815P probably damaging Het
Glrx5 A G 12: 105,006,582 (GRCm39) N111S possibly damaging Het
Gm10845 A G 14: 80,100,614 (GRCm39) noncoding transcript Het
Gm9925 T A 18: 74,198,587 (GRCm39) probably benign Het
Gsdme T C 6: 50,204,339 (GRCm39) N206S probably benign Het
Helz2 T C 2: 180,872,843 (GRCm39) S2459G probably benign Het
Hnrnpul1 A G 7: 25,453,784 (GRCm39) S93P possibly damaging Het
Ints2 A T 11: 86,117,574 (GRCm39) I716N possibly damaging Het
Lmnb2 G A 10: 80,740,962 (GRCm39) Q248* probably null Het
Map3k7cl A G 16: 87,367,209 (GRCm39) I32V probably benign Het
Mfsd4b4 A T 10: 39,768,466 (GRCm39) I255N probably benign Het
Myh6 A G 14: 55,187,965 (GRCm39) I1163T probably benign Het
Ntsr1 T A 2: 180,142,581 (GRCm39) L124Q probably damaging Het
Obscn C T 11: 59,013,445 (GRCm39) probably null Het
P4ha2 G A 11: 54,017,238 (GRCm39) probably null Het
Pcdha9 T A 18: 37,132,164 (GRCm39) V411D probably benign Het
Pkhd1l1 A T 15: 44,389,384 (GRCm39) I1380F probably damaging Het
Plekha1 T C 7: 130,493,983 (GRCm39) V106A probably benign Het
Plekhm1 A T 11: 103,267,517 (GRCm39) V818E possibly damaging Het
Pprc1 T G 19: 46,053,809 (GRCm39) probably benign Het
Prb1c A G 6: 132,339,036 (GRCm39) S61P unknown Het
Prmt9 T C 8: 78,287,647 (GRCm39) probably benign Het
Rab26 T C 17: 24,749,373 (GRCm39) N193D possibly damaging Het
Rnf111 A G 9: 70,336,862 (GRCm39) S942P probably damaging Het
Scgb2b18 T C 7: 32,872,650 (GRCm39) T52A probably damaging Het
Syt3 C T 7: 44,042,187 (GRCm39) Q349* probably null Het
Tas2r107 T C 6: 131,636,743 (GRCm39) N102S probably benign Het
Tas2r126 T A 6: 42,411,934 (GRCm39) Y156N possibly damaging Het
Tcaf2 A T 6: 42,619,712 (GRCm39) I105N probably benign Het
Tet1 A C 10: 62,715,552 (GRCm39) M81R probably benign Het
Togaram2 T C 17: 72,036,200 (GRCm39) Y897H probably damaging Het
Trerf1 A T 17: 47,625,197 (GRCm39) noncoding transcript Het
Ttn G A 2: 76,591,579 (GRCm39) T12703I probably damaging Het
Unc79 A G 12: 103,091,885 (GRCm39) K1735E possibly damaging Het
Usp54 G A 14: 20,633,419 (GRCm39) T372I possibly damaging Het
Wdr24 T C 17: 26,046,102 (GRCm39) S476P probably benign Het
Zbtb1 T C 12: 76,433,049 (GRCm39) I345T possibly damaging Het
Zcrb1 T A 15: 93,293,496 (GRCm39) I29L probably benign Het
Zfp341 T A 2: 154,472,361 (GRCm39) C315S probably damaging Het
Zfp623 C A 15: 75,820,012 (GRCm39) R323S probably benign Het
Zfp831 T A 2: 174,485,885 (GRCm39) Y187N 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
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'- GAAACCCTATCCCGTCCATG -3'
(R):5'- CGTGGATTGGAACTGCTGAC -3'

Sequencing Primer
(F):5'- AAACCCTATCCCGTCCATGTTCAG -3'
(R):5'- TGCTGACAGCCGGAGATCAG -3'
Posted On 2017-03-31