Incidental Mutation 'R4701:Nphp4'
ID 356010
Institutional Source Beutler Lab
Gene Symbol Nphp4
Ensembl Gene ENSMUSG00000039577
Gene Name nephronophthisis 4 (juvenile) homolog (human)
Synonyms nmf192, 4930564O18Rik
MMRRC Submission 041949-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.124) question?
Stock # R4701 (G1)
Quality Score 216
Status Validated
Chromosome 4
Chromosomal Location 152476706-152563183 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to C at 152496659 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 100 (F100S)
Ref Sequence ENSEMBL: ENSMUSP00000080128 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056567] [ENSMUST00000081393]
AlphaFold P59240
Predicted Effect probably damaging
Transcript: ENSMUST00000056567
AA Change: F100S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: F100S

DomainStartEndE-ValueType
low complexity region 317 333 N/A INTRINSIC
low complexity region 367 380 N/A INTRINSIC
low complexity region 473 484 N/A INTRINSIC
low complexity region 507 530 N/A INTRINSIC
low complexity region 896 909 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000081393
AA Change: F100S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: F100S

DomainStartEndE-ValueType
low complexity region 317 333 N/A INTRINSIC
low complexity region 367 380 N/A INTRINSIC
low complexity region 473 484 N/A INTRINSIC
low complexity region 507 530 N/A INTRINSIC
low complexity region 896 909 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142027
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146223
Meta Mutation Damage Score 0.9133 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.6%
Validation Efficiency 96% (108/112)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal disease, and with Senior-Loken syndrome type 4, a combination of nephronophthisis and retinitis pigmentosa. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mutant mice have a mottled retina with photoreceptor degeneration and male infertility associated with oligozoospermia and asthenozoospermia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 97 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aarsd1 T C 11: 101,411,160 (GRCm38) I196V probably benign Het
Aass T A 6: 23,075,856 (GRCm38) K761* probably null Het
Abca13 A G 11: 9,292,306 (GRCm38) T1390A possibly damaging Het
Abhd16a T C 17: 35,096,606 (GRCm38) probably null Het
Acad11 C T 9: 104,095,565 (GRCm38) Q486* probably null Het
Actl9 T C 17: 33,433,935 (GRCm38) L323P probably benign Het
Adam12 T A 7: 133,916,462 (GRCm38) I650F possibly damaging Het
Adgre4 A T 17: 55,784,971 (GRCm38) D77V probably damaging Het
Ankrd26 A G 6: 118,506,485 (GRCm38) F1586S possibly damaging Het
Anpep T C 7: 79,839,465 (GRCm38) T320A probably benign Het
Arl15 T A 13: 113,967,725 (GRCm38) C133S probably benign Het
Ascc3 A G 10: 50,720,664 (GRCm38) N1230S possibly damaging Het
Atf4 T A 15: 80,257,417 (GRCm38) I336K probably damaging Het
Atp7b A T 8: 22,000,121 (GRCm38) S1044T probably benign Het
Atp8b4 A G 2: 126,414,293 (GRCm38) F249L probably damaging Het
AU021092 G T 16: 5,212,193 (GRCm38) N319K probably benign Het
Bbs4 A G 9: 59,323,519 (GRCm38) V440A probably benign Het
Bpifb4 G T 2: 153,950,385 (GRCm38) G450C probably damaging Het
Cadm1 G A 9: 47,818,822 (GRCm38) probably benign Het
Ccser2 G A 14: 36,938,697 (GRCm38) L500F probably damaging Het
Cd22 T A 7: 30,876,153 (GRCm38) I155F probably damaging Het
Cdkl4 A T 17: 80,543,652 (GRCm38) V207E probably damaging Het
Cfap65 T C 1: 74,918,908 (GRCm38) D947G probably damaging Het
Cntn6 T C 6: 104,804,360 (GRCm38) V397A probably benign Het
Cpox T A 16: 58,677,969 (GRCm38) Y388* probably null Het
Dab1 C T 4: 104,731,751 (GRCm38) A524V probably benign Het
Dda1 T A 8: 71,473,810 (GRCm38) Y58N probably damaging Het
Dennd4a C T 9: 64,897,357 (GRCm38) T1326I possibly damaging Het
Eps8l2 A T 7: 141,357,260 (GRCm38) I338F probably damaging Het
Fbxo42 A G 4: 141,199,809 (GRCm38) T467A probably benign Het
Flt4 T C 11: 49,626,808 (GRCm38) F319S possibly damaging Het
Fmn1 A T 2: 113,584,071 (GRCm38) Y895F possibly damaging Het
Gm6887 C A 7: 42,465,093 (GRCm38) noncoding transcript Het
Grid2 A G 6: 64,665,915 (GRCm38) D887G probably benign Het
Grm6 C T 11: 50,863,010 (GRCm38) P714S probably damaging Het
Gsto2 A G 19: 47,884,656 (GRCm38) I157V probably benign Het
Il15ra A G 2: 11,718,345 (GRCm38) probably null Het
Impg1 A G 9: 80,314,400 (GRCm38) F713L probably benign Het
Jag1 T A 2: 137,094,456 (GRCm38) T373S probably benign Het
Kcnh3 T A 15: 99,241,945 (GRCm38) L904Q probably benign Het
Kctd19 C A 8: 105,390,429 (GRCm38) G356V possibly damaging Het
Kdm5b T A 1: 134,606,012 (GRCm38) probably benign Het
Kif1a T C 1: 93,078,835 (GRCm38) I37V probably damaging Het
Lama5 G A 2: 180,191,696 (GRCm38) R1508C probably damaging Het
Lamb1 T A 12: 31,266,848 (GRCm38) C65* probably null Het
Lingo1 A G 9: 56,620,258 (GRCm38) F349S probably damaging Het
Loxl4 G A 19: 42,607,613 (GRCm38) H147Y probably benign Het
Lrrn4cl T A 19: 8,852,055 (GRCm38) N132K probably damaging Het
Med17 A T 9: 15,270,360 (GRCm38) H31Q probably damaging Het
Med23 A T 10: 24,893,648 (GRCm38) L476F probably damaging Het
Mgst1 A T 6: 138,150,838 (GRCm38) D66V probably damaging Het
Mroh2a T C 1: 88,234,612 (GRCm38) probably null Het
Mroh2a A C 1: 88,241,618 (GRCm38) I672L probably benign Het
Muc4 A T 16: 32,755,846 (GRCm38) probably benign Het
Myo18a C T 11: 77,817,665 (GRCm38) T30M probably damaging Het
Ncapg2 G T 12: 116,440,618 (GRCm38) R903L probably benign Het
Nme1 A G 11: 93,965,908 (GRCm38) I9T probably damaging Het
Nmt2 T A 2: 3,322,641 (GRCm38) I357N probably benign Het
Oca2 C A 7: 56,255,002 (GRCm38) T72K probably benign Het
Olfr1411 C A 1: 92,597,438 (GRCm38) D306E probably benign Het
Olfr625-ps1 G A 7: 103,683,062 (GRCm38) V105M probably damaging Het
Olfr676 A T 7: 105,035,591 (GRCm38) D131V probably damaging Het
Olfr677 A T 7: 105,056,879 (GRCm38) D211V probably damaging Het
Olfr871 T C 9: 20,212,625 (GRCm38) I92T probably damaging Het
Plce1 A T 19: 38,725,007 (GRCm38) T1240S probably benign Het
Plch1 A T 3: 63,699,496 (GRCm38) probably null Het
Plxna4 T C 6: 32,516,688 (GRCm38) D331G probably damaging Het
Ppp1r3a T C 6: 14,718,993 (GRCm38) T641A probably benign Het
Rab32 A G 10: 10,550,854 (GRCm38) L116P probably benign Het
Recql4 C T 15: 76,708,585 (GRCm38) C302Y probably damaging Het
Rorc G C 3: 94,391,710 (GRCm38) E391Q probably null Het
Saa4 A T 7: 46,731,627 (GRCm38) F24I possibly damaging Het
Sall1 T A 8: 89,031,160 (GRCm38) K772M probably damaging Het
Sdk1 T G 5: 142,185,231 (GRCm38) L1950V probably damaging Het
Sil1 T C 18: 35,266,896 (GRCm38) E352G probably benign Het
Slc26a3 C T 12: 31,447,774 (GRCm38) P59L probably damaging Het
Smco2 T C 6: 146,861,942 (GRCm38) probably benign Het
Sppl3 A G 5: 115,103,313 (GRCm38) probably null Het
St6gal2 T A 17: 55,496,344 (GRCm38) V360D probably damaging Het
Stard9 G A 2: 120,705,713 (GRCm38) R345Q possibly damaging Het
Susd4 T A 1: 182,892,061 (GRCm38) Y414N probably damaging Het
Tenm4 T C 7: 96,895,349 (GRCm38) Y2191H probably damaging Het
Tln2 A G 9: 67,346,527 (GRCm38) V754A probably benign Het
Tmem132c T A 5: 127,564,496 (GRCm38) probably benign Het
Tnn A T 1: 160,147,768 (GRCm38) S30T possibly damaging Het
Trpd52l3 G T 19: 30,004,495 (GRCm38) V217F probably damaging Het
Trpm1 G T 7: 64,243,500 (GRCm38) L1033F probably damaging Het
Tulp2 A G 7: 45,517,924 (GRCm38) E182G probably damaging Het
Ubr4 A G 4: 139,471,336 (GRCm38) K4490R possibly damaging Het
Usp17la A T 7: 104,860,649 (GRCm38) R154* probably null Het
Vmn2r17 T G 5: 109,427,983 (GRCm38) M240R probably damaging Het
Vmn2r22 T A 6: 123,650,469 (GRCm38) N56I probably benign Het
Wdr66 A G 5: 123,322,613 (GRCm38) K1213E probably benign Het
Zdhhc21 A T 4: 82,820,334 (GRCm38) I206N possibly damaging Het
Zfp148 T A 16: 33,456,908 (GRCm38) D122E probably benign Het
Zfp804a A T 2: 82,256,582 (GRCm38) S252C probably damaging Het
Zgrf1 C T 3: 127,598,704 (GRCm38) T1291I probably benign Het
Other mutations in Nphp4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00922:Nphp4 APN 4 152,537,309 (GRCm38) splice site probably benign
IGL00963:Nphp4 APN 4 152,537,861 (GRCm38) missense probably benign 0.01
IGL01571:Nphp4 APN 4 152,556,382 (GRCm38) missense probably benign 0.21
IGL01707:Nphp4 APN 4 152,538,983 (GRCm38) missense probably benign 0.00
IGL01837:Nphp4 APN 4 152,488,881 (GRCm38) missense probably damaging 0.96
IGL02341:Nphp4 APN 4 152,555,469 (GRCm38) splice site probably benign
IGL02558:Nphp4 APN 4 152,555,531 (GRCm38) missense probably damaging 1.00
IGL02563:Nphp4 APN 4 152,556,220 (GRCm38) missense probably benign 0.00
IGL02712:Nphp4 APN 4 152,556,275 (GRCm38) missense probably damaging 1.00
IGL03023:Nphp4 APN 4 152,524,235 (GRCm38) splice site probably null
R0280:Nphp4 UTSW 4 152,551,936 (GRCm38) splice site probably benign
R0317:Nphp4 UTSW 4 152,551,931 (GRCm38) critical splice donor site probably null
R0410:Nphp4 UTSW 4 152,557,046 (GRCm38) missense probably benign
R0433:Nphp4 UTSW 4 152,518,172 (GRCm38) missense probably benign 0.00
R0706:Nphp4 UTSW 4 152,555,617 (GRCm38) missense probably damaging 0.98
R0785:Nphp4 UTSW 4 152,562,109 (GRCm38) missense possibly damaging 0.58
R0890:Nphp4 UTSW 4 152,498,220 (GRCm38) missense possibly damaging 0.93
R0930:Nphp4 UTSW 4 152,538,055 (GRCm38) missense probably benign 0.01
R1202:Nphp4 UTSW 4 152,488,729 (GRCm38) splice site probably null
R1203:Nphp4 UTSW 4 152,488,832 (GRCm38) missense probably damaging 0.96
R1366:Nphp4 UTSW 4 152,502,926 (GRCm38) missense probably damaging 0.96
R1452:Nphp4 UTSW 4 152,547,018 (GRCm38) missense probably damaging 0.99
R1598:Nphp4 UTSW 4 152,562,090 (GRCm38) missense probably benign 0.00
R1699:Nphp4 UTSW 4 152,496,664 (GRCm38) missense probably damaging 0.99
R2007:Nphp4 UTSW 4 152,554,654 (GRCm38) missense probably damaging 0.97
R2082:Nphp4 UTSW 4 152,559,364 (GRCm38) missense probably benign 0.38
R2264:Nphp4 UTSW 4 152,503,008 (GRCm38) splice site probably benign
R2280:Nphp4 UTSW 4 152,557,043 (GRCm38) missense possibly damaging 0.95
R2281:Nphp4 UTSW 4 152,557,043 (GRCm38) missense possibly damaging 0.95
R2926:Nphp4 UTSW 4 152,518,139 (GRCm38) missense probably damaging 0.99
R3764:Nphp4 UTSW 4 152,538,017 (GRCm38) splice site probably benign
R4084:Nphp4 UTSW 4 152,488,791 (GRCm38) missense probably damaging 1.00
R4091:Nphp4 UTSW 4 152,547,018 (GRCm38) missense probably damaging 0.97
R4240:Nphp4 UTSW 4 152,555,684 (GRCm38) missense probably benign 0.07
R4778:Nphp4 UTSW 4 152,556,291 (GRCm38) missense probably benign 0.44
R4783:Nphp4 UTSW 4 152,554,546 (GRCm38) missense probably benign 0.00
R4784:Nphp4 UTSW 4 152,554,546 (GRCm38) missense probably benign 0.00
R4974:Nphp4 UTSW 4 152,537,793 (GRCm38) missense probably damaging 1.00
R5053:Nphp4 UTSW 4 152,544,462 (GRCm38) splice site probably null
R5117:Nphp4 UTSW 4 152,524,232 (GRCm38) splice site probably null
R5128:Nphp4 UTSW 4 152,502,991 (GRCm38) missense probably benign 0.01
R5665:Nphp4 UTSW 4 152,506,485 (GRCm38) missense probably benign 0.25
R5890:Nphp4 UTSW 4 152,547,079 (GRCm38) missense probably benign 0.44
R6171:Nphp4 UTSW 4 152,544,449 (GRCm38) missense probably damaging 0.99
R6601:Nphp4 UTSW 4 152,503,007 (GRCm38) splice site probably null
R6772:Nphp4 UTSW 4 152,544,406 (GRCm38) missense probably benign 0.07
R6806:Nphp4 UTSW 4 152,538,101 (GRCm38) missense probably benign 0.02
R7006:Nphp4 UTSW 4 152,488,802 (GRCm38) missense probably benign 0.12
R7124:Nphp4 UTSW 4 152,555,684 (GRCm38) missense probably benign 0.07
R7381:Nphp4 UTSW 4 152,499,003 (GRCm38) missense possibly damaging 0.94
R7411:Nphp4 UTSW 4 152,554,717 (GRCm38) missense probably benign 0.25
R7638:Nphp4 UTSW 4 152,554,534 (GRCm38) missense probably benign 0.08
R7814:Nphp4 UTSW 4 152,544,403 (GRCm38) missense probably damaging 1.00
R7814:Nphp4 UTSW 4 152,524,272 (GRCm38) missense possibly damaging 0.93
R7841:Nphp4 UTSW 4 152,496,683 (GRCm38) missense probably benign 0.01
R8346:Nphp4 UTSW 4 152,561,321 (GRCm38) missense probably damaging 1.00
R8479:Nphp4 UTSW 4 152,524,290 (GRCm38) missense probably benign 0.01
R8847:Nphp4 UTSW 4 152,506,406 (GRCm38) missense probably damaging 1.00
R8995:Nphp4 UTSW 4 152,538,888 (GRCm38) missense probably damaging 1.00
R8997:Nphp4 UTSW 4 152,538,888 (GRCm38) missense probably damaging 1.00
R9075:Nphp4 UTSW 4 152,507,448 (GRCm38) missense probably damaging 1.00
R9089:Nphp4 UTSW 4 152,561,216 (GRCm38) missense possibly damaging 0.87
R9191:Nphp4 UTSW 4 152,556,230 (GRCm38) missense probably damaging 1.00
R9274:Nphp4 UTSW 4 152,555,599 (GRCm38) missense probably benign 0.05
R9311:Nphp4 UTSW 4 152,524,257 (GRCm38) missense probably damaging 0.99
R9383:Nphp4 UTSW 4 152,544,461 (GRCm38) critical splice donor site probably null
R9628:Nphp4 UTSW 4 152,484,509 (GRCm38) missense probably damaging 1.00
R9711:Nphp4 UTSW 4 152,538,977 (GRCm38) missense possibly damaging 0.77
R9712:Nphp4 UTSW 4 152,547,064 (GRCm38) missense probably benign 0.17
R9752:Nphp4 UTSW 4 152,537,280 (GRCm38) missense probably benign 0.00
R9790:Nphp4 UTSW 4 152,562,148 (GRCm38) missense probably null 0.64
R9791:Nphp4 UTSW 4 152,562,148 (GRCm38) missense probably null 0.64
T0970:Nphp4 UTSW 4 152,556,379 (GRCm38) missense probably damaging 1.00
X0058:Nphp4 UTSW 4 152,559,707 (GRCm38) missense possibly damaging 0.95
Z1177:Nphp4 UTSW 4 152,518,196 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCGTGTTGAACTGAACTAGGC -3'
(R):5'- GAGTACTGTTTACCGTTTGTCC -3'

Sequencing Primer
(F):5'- GTATGAACTCCAGCTCCTGAG -3'
(R):5'- TGTCCTGGGCTGCAGAG -3'
Posted On 2015-10-21