Incidental Mutation 'R9274:Nphp4'
ID 703152
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 # R9274 (G1)
Quality Score 225.009
Status Validated
Chromosome 4
Chromosomal Location 152561163-152647640 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 152640056 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 981 (Y981H)
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: Y981H

PolyPhen 2 Score 0.046 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: Y981H

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: Y981H

PolyPhen 2 Score 0.046 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: Y981H

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: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (65/65)
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actc1 A T 2: 113,879,752 (GRCm39) S236T probably benign Het
Adam30 A G 3: 98,069,267 (GRCm39) T239A probably benign Het
Aoc1l2 T C 6: 48,907,341 (GRCm39) F114L possibly damaging Het
Ascl2 G A 7: 142,521,753 (GRCm39) R232C probably damaging Het
Atp10a C A 7: 58,478,369 (GRCm39) Q1471K probably benign Het
Avl9 T A 6: 56,720,346 (GRCm39) D461E probably damaging Het
Baiap3 T A 17: 25,463,354 (GRCm39) Y983F probably damaging Het
C1rl A G 6: 124,485,483 (GRCm39) S285G probably benign Het
Cacna1i G A 15: 80,254,354 (GRCm39) V772M probably damaging Het
Ccser2 T A 14: 36,660,737 (GRCm39) D472V possibly damaging Het
Cd244a T G 1: 171,401,928 (GRCm39) V218G probably benign Het
Cdhr1 T C 14: 36,802,564 (GRCm39) K633R probably benign Het
Col14a1 A G 15: 55,381,671 (GRCm39) Q1748R probably damaging Het
Col6a3 T A 1: 90,707,020 (GRCm39) Y2638F unknown Het
Crnkl1 A T 2: 145,765,836 (GRCm39) F411L probably damaging Het
Crp T A 1: 172,526,072 (GRCm39) F52L possibly damaging Het
Dnah12 A G 14: 26,537,374 (GRCm39) N2208D probably benign Het
Exd2 T C 12: 80,539,674 (GRCm39) probably null Het
F13a1 A T 13: 37,052,761 (GRCm39) I726N probably damaging Het
Fmo6 G A 1: 162,747,921 (GRCm39) T381I probably benign Het
Gdpd5 T C 7: 99,107,989 (GRCm39) L522P probably damaging Het
Gm12790 T A 4: 101,824,743 (GRCm39) D175V possibly damaging Het
Gm3543 T C 14: 41,802,125 (GRCm39) R120G probably damaging Het
Gpatch2 T A 1: 186,963,029 (GRCm39) D273E probably damaging Het
Hlcs A G 16: 94,088,785 (GRCm39) S66P possibly damaging Het
Hmcn1 T C 1: 150,506,046 (GRCm39) T3827A probably benign Het
Ism2 G A 12: 87,331,827 (GRCm39) Q237* probably null Het
Jph2 G A 2: 163,239,547 (GRCm39) probably benign Het
Kcnb2 A G 1: 15,781,723 (GRCm39) Q865R probably benign Het
Kcnh6 C G 11: 105,924,860 (GRCm39) H941Q possibly damaging Het
Kcnk9 A G 15: 72,384,224 (GRCm39) V318A unknown Het
Lemd3 G A 10: 120,814,717 (GRCm39) A172V possibly damaging Het
Lifr G T 15: 7,217,591 (GRCm39) A840S probably damaging Het
Lnpep T C 17: 17,758,837 (GRCm39) T836A probably benign Het
Mapk13 A G 17: 28,988,490 (GRCm39) Y36C probably damaging Het
Mdm2 G A 10: 117,541,081 (GRCm39) probably benign Het
Msmb T C 14: 31,870,130 (GRCm39) M34T probably benign Het
Myo5a A G 9: 75,097,279 (GRCm39) N1319S possibly damaging Het
Myot T A 18: 44,479,265 (GRCm39) V334E probably damaging Het
Nalcn A G 14: 123,753,068 (GRCm39) I306T probably damaging Het
Nicn1 C T 9: 108,171,708 (GRCm39) R163C possibly damaging Het
Nphs2 G A 1: 156,144,416 (GRCm39) R140Q probably damaging Het
Nsa2 C T 13: 97,272,170 (GRCm39) R17H probably benign Het
Nup98 C A 7: 101,788,037 (GRCm39) R1011L probably benign Het
Obox6 T C 7: 15,567,766 (GRCm39) H227R possibly damaging Het
Or10ak14 G A 4: 118,610,883 (GRCm39) A286V probably benign Het
Or1j14 T C 2: 36,417,559 (GRCm39) I45T probably damaging Het
Or4c1 A C 2: 89,133,513 (GRCm39) L141R probably damaging Het
P2rx2 C T 5: 110,489,709 (GRCm39) G202D probably damaging Het
Pcdh12 A G 18: 38,415,950 (GRCm39) W392R probably damaging Het
Plxna2 G A 1: 194,471,136 (GRCm39) G969D probably damaging Het
Prg4 T C 1: 150,331,924 (GRCm39) T250A possibly damaging Het
Rad54l G T 4: 115,967,667 (GRCm39) P205Q probably damaging Het
Ralgapb A G 2: 158,278,539 (GRCm39) I334M probably damaging Het
Ric3 C T 7: 108,647,212 (GRCm39) D204N probably damaging Het
Rnf10 A T 5: 115,385,322 (GRCm39) Y557* probably null Het
Ruvbl1 A G 6: 88,474,334 (GRCm39) I446V probably benign Het
Serinc3 A T 2: 163,468,371 (GRCm39) V361D probably damaging Het
Slc4a1 C A 11: 102,242,047 (GRCm39) V864L probably benign Het
Slf1 C A 13: 77,191,669 (GRCm39) *1055L probably null Het
Stk25 T C 1: 93,552,806 (GRCm39) S328G probably benign Het
Stpg1 T C 4: 135,252,782 (GRCm39) F178L possibly damaging Het
Tmem25 C T 9: 44,706,336 (GRCm39) R345H probably benign Het
Tssk1 A T 16: 17,712,724 (GRCm39) I170L probably benign Het
Tubg1 A G 11: 101,017,241 (GRCm39) probably benign Het
Uchl3 A G 14: 101,903,240 (GRCm39) D33G probably damaging Het
Vmn1r152 A T 7: 22,223,056 (GRCm39) H222L probably benign Het
Zfp975 C T 7: 42,312,299 (GRCm39) V105I 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
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
R9752:Nphp4 UTSW 4 152,621,737 (GRCm39) missense probably benign 0.00
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'- AGCTGGGACATGGTGTTCAC -3'
(R):5'- TAGAACTGTCCAACGCCCAGAG -3'

Sequencing Primer
(F):5'- GGACATGGTGTTCACCAGATG -3'
(R):5'- ACAGTTGGCTGGGTCACATACAC -3'
Posted On 2022-03-25