Incidental Mutation 'R5272:Nphs1'
ID 486797
Institutional Source Beutler Lab
Gene Symbol Nphs1
Ensembl Gene ENSMUSG00000006649
Gene Name nephrosis 1, nephrin
Synonyms nephrin
MMRRC Submission 042836-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5272 (G1)
Quality Score 217
Status Not validated
Chromosome 7
Chromosomal Location 30157740-30186648 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 30181067 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 1096 (E1096G)
Ref Sequence ENSEMBL: ENSMUSP00000116500 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006825] [ENSMUST00000126297]
AlphaFold Q9QZS7
Predicted Effect probably benign
Transcript: ENSMUST00000006825
AA Change: E1110G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: E1110G

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 possibly damaging
Transcript: ENSMUST00000126297
AA Change: E1096G

PolyPhen 2 Score 0.856 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: E1096G

DomainStartEndE-ValueType
IG 38 132 1.38e-6 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131004
Predicted Effect probably benign
Transcript: ENSMUST00000149086
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208689
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.4%
  • 20x: 93.0%
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actl6a A G 3: 32,772,759 (GRCm39) E245G probably damaging Het
Arsb A T 13: 93,930,670 (GRCm39) T213S possibly damaging Het
Cep152 G A 2: 125,452,950 (GRCm39) T374I probably benign Het
Crx C T 7: 15,602,210 (GRCm39) C156Y probably damaging Het
Csmd1 T A 8: 16,249,958 (GRCm39) T1007S probably damaging Het
Cyp19a1 A T 9: 54,083,898 (GRCm39) C164S probably benign Het
Ddx55 A T 5: 124,696,092 (GRCm39) I137F possibly damaging Het
Dgkg C A 16: 22,407,044 (GRCm39) probably null Het
Dicer1 A G 12: 104,670,499 (GRCm39) I1022T probably damaging Het
Dis3l2 T C 1: 86,901,126 (GRCm39) V439A possibly damaging Het
Dnah5 T C 15: 28,350,811 (GRCm39) V2611A probably benign Het
Dnah6 A G 6: 73,104,844 (GRCm39) probably null Het
Ercc6 A T 14: 32,240,985 (GRCm39) K170* probably null Het
Fibcd1 A T 2: 31,706,635 (GRCm39) C399S probably damaging Het
Fibcd1 G T 2: 31,706,636 (GRCm39) N398K probably damaging Het
Fnbp4 G A 2: 90,583,459 (GRCm39) M327I probably benign Het
Fryl A T 5: 73,222,479 (GRCm39) L256* probably null Het
Galr1 T A 18: 82,423,761 (GRCm39) Y172F probably benign Het
Gpi1 T C 7: 33,920,115 (GRCm39) N186S probably damaging Het
Kcnh8 A G 17: 53,212,043 (GRCm39) I614V probably damaging Het
Krt23 A T 11: 99,369,099 (GRCm39) I398N probably damaging Het
Mia3 G A 1: 183,109,125 (GRCm39) R656* probably null Het
Mup6 G C 4: 60,005,922 (GRCm39) G138A probably damaging Het
Nectin3 A G 16: 46,268,839 (GRCm39) V521A possibly damaging Het
Nhsl3 T C 4: 129,118,005 (GRCm39) T208A possibly damaging Het
Or8s5 G A 15: 98,238,246 (GRCm39) A208V probably benign Het
Panx1 C T 9: 14,956,152 (GRCm39) probably null Het
Pcdhb4 A G 18: 37,440,819 (GRCm39) Y43C probably benign Het
Plbd1 A G 6: 136,617,156 (GRCm39) Y62H probably damaging Het
Rab40b A G 11: 121,248,134 (GRCm39) V190A probably damaging Het
Ryr3 T C 2: 112,483,558 (GRCm39) E4063G probably damaging Het
Smlr1 T C 10: 25,411,925 (GRCm39) I21V probably benign Het
Tenm4 T A 7: 96,523,410 (GRCm39) Y1614N probably damaging Het
Tesmin C A 19: 3,456,992 (GRCm39) A257E probably damaging Het
Tgif1 A G 17: 71,153,249 (GRCm39) L34P probably damaging Het
Ticrr C A 7: 79,319,353 (GRCm39) T446K probably benign Het
Tmc7 A G 7: 118,160,276 (GRCm39) I187T probably benign Het
Tpst2 T A 5: 112,455,818 (GRCm39) V119E probably damaging Het
Trf A T 9: 103,105,177 (GRCm39) M45K probably damaging Het
Trim45 T C 3: 100,837,235 (GRCm39) C524R probably damaging Het
Ttc27 G A 17: 75,049,972 (GRCm39) V293I probably damaging Het
Ugt1a6b C T 1: 88,034,949 (GRCm39) R96C possibly damaging Het
Vit A G 17: 78,894,264 (GRCm39) Q222R probably benign Het
Zfp148 T A 16: 33,316,594 (GRCm39) V380D 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
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
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'- TCCAATGCCTCCTGTGTTGG -3'
(R):5'- GCTTGAAGCTGAGACTGGAG -3'

Sequencing Primer
(F):5'- CCTGTGTTGGGGGACTCCTC -3'
(R):5'- AGCTGAGACTGGAGGCTGC -3'
Posted On 2017-08-17