Incidental Mutation 'R9752:Nphp4'
ID 732562
Institutional Source Beutler Lab
Gene Symbol Nphp4
Ensembl Gene ENSMUSG00000039577
Gene Name nephronophthisis 4 (juvenile) homolog (human)
Synonyms nmf192, 4930564O18Rik
MMRRC Submission
Accession Numbers
Essential gene? Probably non essential (E-score: 0.142) question?
Stock # R9752 (G1)
Quality Score 225.009
Status Not validated
Chromosome 4
Chromosomal Location 152561163-152647640 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 152621737 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 531 (E531G)
Ref Sequence ENSEMBL: ENSMUSP00000049920 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056567] [ENSMUST00000081393]
AlphaFold P59240
Predicted Effect probably benign
Transcript: ENSMUST00000056567
AA Change: E531G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: E531G

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 benign
Transcript: ENSMUST00000081393
AA Change: E531G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: E531G

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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 99.3%
  • 20x: 98.4%
Validation Efficiency
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ano2 C T 6: 125,840,499 (GRCm39) T390I probably damaging Het
Cc2d2b T C 19: 40,781,271 (GRCm39) V772A probably damaging Het
Cd109 A G 9: 78,614,834 (GRCm39) I1294V probably benign Het
Cic A G 7: 24,971,403 (GRCm39) E378G probably damaging Het
Clhc1 C T 11: 29,507,778 (GRCm39) P175L probably benign Het
Clip1 T C 5: 123,760,009 (GRCm39) E783G probably damaging Het
Cnot1 A G 8: 96,488,019 (GRCm39) Y546H probably damaging Het
Cog7 C A 7: 121,580,639 (GRCm39) probably null Het
Cr2 T C 1: 194,823,575 (GRCm39) T1008A probably benign Het
Diaph1 T C 18: 38,036,124 (GRCm39) T196A unknown Het
Entr1 T C 2: 26,276,990 (GRCm39) N247D probably benign Het
Flg2 A T 3: 93,108,467 (GRCm39) D165V probably damaging Het
Fstl1 T G 16: 37,649,534 (GRCm39) N249K probably damaging Het
Gatad2a A G 8: 70,364,839 (GRCm39) V515A probably benign Het
Gbp2b A T 3: 142,313,917 (GRCm39) D399V probably benign Het
Gna14 G A 19: 16,586,781 (GRCm39) V319I probably benign Het
Grip1 A G 10: 119,871,256 (GRCm39) D661G possibly damaging Het
Gtf3c4 C A 2: 28,724,126 (GRCm39) L535F probably damaging Het
Haus8 A C 8: 71,715,731 (GRCm39) S36A probably damaging Het
Hectd4 A T 5: 121,448,744 (GRCm39) Y364F probably benign Het
Hectd4 C T 5: 121,472,415 (GRCm39) A2717V possibly damaging Het
Hsf5 C T 11: 87,513,709 (GRCm39) T258M probably benign Het
Ifi209 A T 1: 173,472,235 (GRCm39) I359F probably damaging Het
Ighmbp2 A G 19: 3,324,360 (GRCm39) V302A probably benign Het
Iqgap3 C A 3: 88,016,176 (GRCm39) F986L probably damaging Het
Itgav T A 2: 83,600,451 (GRCm39) probably null Het
Kcp A T 6: 29,497,754 (GRCm39) D502E probably damaging Het
Kif15 T C 9: 122,824,890 (GRCm39) probably null Het
Lipo2 C G 19: 33,723,221 (GRCm39) K189N possibly damaging Het
Lrch4 T A 5: 137,636,218 (GRCm39) S390T probably benign Het
Mast2 G T 4: 116,179,508 (GRCm39) H389N probably benign Het
Med13 A G 11: 86,174,147 (GRCm39) Y1784H possibly damaging Het
Micu3 A G 8: 40,833,751 (GRCm39) K462E possibly damaging Het
Mrps10 T C 17: 47,683,572 (GRCm39) probably null Het
Msh6 T C 17: 88,293,963 (GRCm39) L906P probably damaging Het
Nrp2 A T 1: 62,851,726 (GRCm39) Y825F probably benign Het
Ntn1 C T 11: 68,276,712 (GRCm39) V79M possibly damaging Het
Nxnl2 A G 13: 51,325,507 (GRCm39) D50G probably damaging Het
Or1e16 T A 11: 73,286,479 (GRCm39) Y123F possibly damaging Het
Or2t26 T C 11: 49,039,681 (GRCm39) M199T probably benign Het
Or52h9 A T 7: 104,202,530 (GRCm39) I135F possibly damaging Het
Or52r1c T A 7: 102,735,669 (GRCm39) C310S probably benign Het
Or6c219 T C 10: 129,780,990 (GRCm39) R314G probably benign Het
Or7e176 G A 9: 20,171,204 (GRCm39) V23I probably benign Het
Ppp1r42 A G 1: 10,073,674 (GRCm39) probably benign Het
Ppp4r3a A T 12: 101,008,763 (GRCm39) N692K probably benign Het
Prr11 T C 11: 86,994,416 (GRCm39) T77A possibly damaging Het
Resf1 T A 6: 149,228,068 (GRCm39) N371K probably benign Het
Rrn3 A G 16: 13,631,095 (GRCm39) I644V probably benign Het
Scd4 T C 19: 44,322,475 (GRCm39) S23P probably benign Het
Slc26a2 T A 18: 61,335,010 (GRCm39) S148C probably benign Het
Slc7a8 T C 14: 54,995,931 (GRCm39) E157G probably benign Het
Spi1 A G 2: 90,943,666 (GRCm39) H70R probably benign Het
Styk1 CTCTTCATGATTTTCTT CTCTT 6: 131,278,612 (GRCm39) probably benign Het
Tlr4 A G 4: 66,757,912 (GRCm39) N235S probably benign Het
Trpc6 C A 9: 8,643,641 (GRCm39) S475R probably benign Het
Usp34 C T 11: 23,409,182 (GRCm39) P2674L probably benign Het
Usp48 G A 4: 137,341,137 (GRCm39) G379D probably damaging Het
Vkorc1l1 T A 5: 130,011,078 (GRCm39) C97* probably null Het
Wfikkn2 T C 11: 94,129,211 (GRCm39) E310G probably benign Het
Zfp266 T A 9: 20,411,496 (GRCm39) N227I probably benign Het
Zfp335 C T 2: 164,749,347 (GRCm39) probably null Het
Zfp677 T A 17: 21,618,511 (GRCm39) C523S probably damaging Het
Zrsr2 GCTCCTCCTCCTCCTCCT GCTCCTCCTCCTCCT X: 162,719,750 (GRCm39) probably benign Het
Other mutations in Nphp4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00922:Nphp4 APN 4 152,621,766 (GRCm39) splice site probably benign
IGL00963:Nphp4 APN 4 152,622,318 (GRCm39) missense probably benign 0.01
IGL01571:Nphp4 APN 4 152,640,839 (GRCm39) missense probably benign 0.21
IGL01707:Nphp4 APN 4 152,623,440 (GRCm39) missense probably benign 0.00
IGL01837:Nphp4 APN 4 152,573,338 (GRCm39) missense probably damaging 0.96
IGL02341:Nphp4 APN 4 152,639,926 (GRCm39) splice site probably benign
IGL02558:Nphp4 APN 4 152,639,988 (GRCm39) missense probably damaging 1.00
IGL02563:Nphp4 APN 4 152,640,677 (GRCm39) missense probably benign 0.00
IGL02712:Nphp4 APN 4 152,640,732 (GRCm39) missense probably damaging 1.00
IGL03023:Nphp4 APN 4 152,608,692 (GRCm39) splice site probably null
R0280:Nphp4 UTSW 4 152,636,393 (GRCm39) splice site probably benign
R0317:Nphp4 UTSW 4 152,636,388 (GRCm39) critical splice donor site probably null
R0410:Nphp4 UTSW 4 152,641,503 (GRCm39) missense probably benign
R0433:Nphp4 UTSW 4 152,602,629 (GRCm39) missense probably benign 0.00
R0706:Nphp4 UTSW 4 152,640,074 (GRCm39) missense probably damaging 0.98
R0785:Nphp4 UTSW 4 152,646,566 (GRCm39) missense possibly damaging 0.58
R0890:Nphp4 UTSW 4 152,582,677 (GRCm39) missense possibly damaging 0.93
R0930:Nphp4 UTSW 4 152,622,512 (GRCm39) missense probably benign 0.01
R1202:Nphp4 UTSW 4 152,573,186 (GRCm39) splice site probably null
R1203:Nphp4 UTSW 4 152,573,289 (GRCm39) missense probably damaging 0.96
R1366:Nphp4 UTSW 4 152,587,383 (GRCm39) missense probably damaging 0.96
R1452:Nphp4 UTSW 4 152,631,475 (GRCm39) missense probably damaging 0.99
R1598:Nphp4 UTSW 4 152,646,547 (GRCm39) missense probably benign 0.00
R1699:Nphp4 UTSW 4 152,581,121 (GRCm39) missense probably damaging 0.99
R2007:Nphp4 UTSW 4 152,639,111 (GRCm39) missense probably damaging 0.97
R2082:Nphp4 UTSW 4 152,643,821 (GRCm39) missense probably benign 0.38
R2264:Nphp4 UTSW 4 152,587,465 (GRCm39) splice site probably benign
R2280:Nphp4 UTSW 4 152,641,500 (GRCm39) missense possibly damaging 0.95
R2281:Nphp4 UTSW 4 152,641,500 (GRCm39) missense possibly damaging 0.95
R2926:Nphp4 UTSW 4 152,602,596 (GRCm39) missense probably damaging 0.99
R3764:Nphp4 UTSW 4 152,622,474 (GRCm39) splice site probably benign
R4084:Nphp4 UTSW 4 152,573,248 (GRCm39) missense probably damaging 1.00
R4091:Nphp4 UTSW 4 152,631,475 (GRCm39) missense probably damaging 0.97
R4240:Nphp4 UTSW 4 152,640,141 (GRCm39) missense probably benign 0.07
R4701:Nphp4 UTSW 4 152,581,116 (GRCm39) missense probably damaging 1.00
R4778:Nphp4 UTSW 4 152,640,748 (GRCm39) missense probably benign 0.44
R4783:Nphp4 UTSW 4 152,639,003 (GRCm39) missense probably benign 0.00
R4784:Nphp4 UTSW 4 152,639,003 (GRCm39) missense probably benign 0.00
R4974:Nphp4 UTSW 4 152,622,250 (GRCm39) missense probably damaging 1.00
R5053:Nphp4 UTSW 4 152,628,919 (GRCm39) splice site probably null
R5117:Nphp4 UTSW 4 152,608,689 (GRCm39) splice site probably null
R5128:Nphp4 UTSW 4 152,587,448 (GRCm39) missense probably benign 0.01
R5665:Nphp4 UTSW 4 152,590,942 (GRCm39) missense probably benign 0.25
R5890:Nphp4 UTSW 4 152,631,536 (GRCm39) missense probably benign 0.44
R6171:Nphp4 UTSW 4 152,628,906 (GRCm39) missense probably damaging 0.99
R6601:Nphp4 UTSW 4 152,587,464 (GRCm39) splice site probably null
R6772:Nphp4 UTSW 4 152,628,863 (GRCm39) missense probably benign 0.07
R6806:Nphp4 UTSW 4 152,622,558 (GRCm39) missense probably benign 0.02
R7006:Nphp4 UTSW 4 152,573,259 (GRCm39) missense probably benign 0.12
R7124:Nphp4 UTSW 4 152,640,141 (GRCm39) missense probably benign 0.07
R7381:Nphp4 UTSW 4 152,583,460 (GRCm39) missense possibly damaging 0.94
R7411:Nphp4 UTSW 4 152,639,174 (GRCm39) missense probably benign 0.25
R7638:Nphp4 UTSW 4 152,638,991 (GRCm39) missense probably benign 0.08
R7814:Nphp4 UTSW 4 152,628,860 (GRCm39) missense probably damaging 1.00
R7814:Nphp4 UTSW 4 152,608,729 (GRCm39) missense possibly damaging 0.93
R7841:Nphp4 UTSW 4 152,581,140 (GRCm39) missense probably benign 0.01
R8346:Nphp4 UTSW 4 152,645,778 (GRCm39) missense probably damaging 1.00
R8479:Nphp4 UTSW 4 152,608,747 (GRCm39) missense probably benign 0.01
R8847:Nphp4 UTSW 4 152,590,863 (GRCm39) missense probably damaging 1.00
R8995:Nphp4 UTSW 4 152,623,345 (GRCm39) missense probably damaging 1.00
R8997:Nphp4 UTSW 4 152,623,345 (GRCm39) missense probably damaging 1.00
R9075:Nphp4 UTSW 4 152,591,905 (GRCm39) missense probably damaging 1.00
R9089:Nphp4 UTSW 4 152,645,673 (GRCm39) missense possibly damaging 0.87
R9191:Nphp4 UTSW 4 152,640,687 (GRCm39) missense probably damaging 1.00
R9274:Nphp4 UTSW 4 152,640,056 (GRCm39) missense probably benign 0.05
R9311:Nphp4 UTSW 4 152,608,714 (GRCm39) missense probably damaging 0.99
R9383:Nphp4 UTSW 4 152,628,918 (GRCm39) critical splice donor site probably null
R9628:Nphp4 UTSW 4 152,568,966 (GRCm39) missense probably damaging 1.00
R9711:Nphp4 UTSW 4 152,623,434 (GRCm39) missense possibly damaging 0.77
R9712:Nphp4 UTSW 4 152,631,521 (GRCm39) missense probably benign 0.17
R9790:Nphp4 UTSW 4 152,646,605 (GRCm39) missense probably null 0.64
R9791:Nphp4 UTSW 4 152,646,605 (GRCm39) missense probably null 0.64
T0970:Nphp4 UTSW 4 152,640,836 (GRCm39) missense probably damaging 1.00
X0058:Nphp4 UTSW 4 152,644,164 (GRCm39) missense possibly damaging 0.95
Z1177:Nphp4 UTSW 4 152,602,653 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CATCATTCTCACACATGCGC -3'
(R):5'- TAGGGCATCACGTTCCTGTC -3'

Sequencing Primer
(F):5'- TCACACATGCGCGCACG -3'
(R):5'- TGTCCTGTCTCAGACGCG -3'
Posted On 2022-11-14