Incidental Mutation 'R5681:Nphs1'
ID 443038
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 # R5681 (G1)
Quality Score 225
Status Not validated
Chromosome 7
Chromosomal Location 30157740-30186648 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 30186050 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 1227 (D1227G)
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: D1227G

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: D1227G

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 benign
Transcript: ENSMUST00000126297
AA Change: D1213G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
AA Change: D1213G

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: 99.6%
  • 3x: 98.8%
  • 10x: 97.0%
  • 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: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acoxl T C 2: 127,814,559 (GRCm39) F45S possibly damaging Het
Adora2b T A 11: 62,140,067 (GRCm39) V47E probably damaging Het
Amdhd2 A G 17: 24,375,014 (GRCm39) I396T probably damaging Het
Arhgap5 G A 12: 52,566,562 (GRCm39) D1178N probably benign Het
Atp10d T C 5: 72,404,289 (GRCm39) probably benign Het
Baiap3 A G 17: 25,468,347 (GRCm39) S264P probably damaging Het
Brinp3 A T 1: 146,777,484 (GRCm39) I644F probably benign Het
Ccdc168 A T 1: 44,100,624 (GRCm39) V158D possibly damaging Het
Ccdc66 T C 14: 27,208,698 (GRCm39) R675G probably benign Het
Cnr2 T G 4: 135,644,000 (GRCm39) M26R probably damaging Het
Col6a2 A T 10: 76,445,085 (GRCm39) probably null Het
Cux1 A G 5: 136,337,038 (GRCm39) W696R probably damaging Het
D6Ertd527e A G 6: 87,088,188 (GRCm39) N117S unknown Het
Dnah12 T C 14: 26,537,452 (GRCm39) C2234R probably benign Het
Dnhd1 G A 7: 105,352,416 (GRCm39) R2523Q probably damaging Het
Dock2 T G 11: 34,199,836 (GRCm39) I1405L probably benign Het
Dsg1c T C 18: 20,416,270 (GRCm39) F724L probably damaging Het
Elapor2 T A 5: 9,509,308 (GRCm39) probably null Het
Enoph1 T C 5: 100,210,136 (GRCm39) probably null Het
Epha10 A T 4: 124,796,359 (GRCm39) Q356L unknown Het
Fbln2 G T 6: 91,248,778 (GRCm39) V1148L probably damaging Het
Firrm T C 1: 163,789,654 (GRCm39) N627S probably damaging Het
Gp2 C T 7: 119,051,517 (GRCm39) V233M possibly damaging Het
Gtf2ird1 T A 5: 134,392,172 (GRCm39) S800C probably damaging Het
Hat1 A G 2: 71,264,553 (GRCm39) probably null Het
Hpdl A T 4: 116,678,039 (GRCm39) S141T probably benign Het
Klhl29 A G 12: 5,140,669 (GRCm39) S658P possibly damaging Het
Lifr T A 15: 7,220,565 (GRCm39) I1065N probably damaging Het
Lrrn2 G T 1: 132,864,899 (GRCm39) probably benign Het
Marchf9 T A 10: 126,894,172 (GRCm39) I144F probably benign Het
Mtnr1a A G 8: 45,540,974 (GRCm39) I312V possibly damaging Het
Ngf T A 3: 102,427,669 (GRCm39) F139L probably damaging Het
Nipbl T C 15: 8,330,866 (GRCm39) I2318V probably benign Het
Nkpd1 C T 7: 19,257,498 (GRCm39) Q276* probably null Het
Olfm3 C A 3: 114,915,924 (GRCm39) N285K probably benign Het
Or1j1 C A 2: 36,702,693 (GRCm39) S137I probably benign Het
Or4f60 T A 2: 111,902,722 (GRCm39) I69F probably benign Het
Or7g35 G A 9: 19,496,195 (GRCm39) D121N probably damaging Het
Or8b12i A G 9: 20,082,091 (GRCm39) Y259H probably damaging Het
Or8b39 C T 9: 37,996,927 (GRCm39) S265F possibly damaging Het
Osbp2 A G 11: 3,813,486 (GRCm39) S128P probably benign Het
Otop2 A T 11: 115,217,685 (GRCm39) M174L probably damaging Het
Pard3 A G 8: 128,115,914 (GRCm39) T668A possibly damaging Het
Pkhd1 T C 1: 20,617,685 (GRCm39) T967A possibly damaging Het
Pls1 A G 9: 95,669,065 (GRCm39) V52A probably damaging Het
Ptcd3 T C 6: 71,884,643 (GRCm39) K64R probably damaging Het
Pxn T C 5: 115,682,593 (GRCm39) W69R possibly damaging Het
Rai14 T C 15: 10,575,206 (GRCm39) D584G probably damaging Het
Safb G A 17: 56,906,000 (GRCm39) probably benign Het
Serinc2 A C 4: 130,158,869 (GRCm39) L10R probably damaging Het
Serpinb12 A T 1: 106,874,431 (GRCm39) H52L probably benign Het
Serpinb9h G A 13: 33,579,812 (GRCm39) C20Y probably damaging Het
Serpinf2 A G 11: 75,326,765 (GRCm39) Y273H probably damaging Het
Slc2a10 T A 2: 165,356,660 (GRCm39) S107T probably benign Het
Slc41a3 T C 6: 90,617,928 (GRCm39) L318P probably damaging Het
Slc6a3 A T 13: 73,686,854 (GRCm39) I74F probably damaging Het
Snrnp200 G A 2: 127,067,055 (GRCm39) G788D probably damaging Het
Snx7 A G 3: 117,640,272 (GRCm39) I79T probably benign Het
Sox11 G T 12: 27,391,823 (GRCm39) D195E probably benign Het
Ssc4d A G 5: 135,999,074 (GRCm39) L43P probably damaging Het
Tab2 A G 10: 7,795,837 (GRCm39) I215T probably damaging Het
Ttn C T 2: 76,660,942 (GRCm39) V7422I possibly damaging Het
Unc13c A T 9: 73,453,357 (GRCm39) probably null Het
Wdr17 T C 8: 55,115,904 (GRCm39) D633G probably damaging Het
Wdsub1 A T 2: 59,683,239 (GRCm39) M445K probably damaging Het
Xpc A G 6: 91,481,102 (GRCm39) F257L 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
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'- GCAAGCCGGTGTGCTAAATC -3'
(R):5'- TTTGTACGGATTTCCTCAGGTC -3'

Sequencing Primer
(F):5'- GCCGGTGTGCTAAATCATCAAGC -3'
(R):5'- GGTCTTCTCCTGAAAAAGACTGTG -3'
Posted On 2016-11-09