Incidental Mutation 'R9089:Nphp4'
ID 690806
Institutional Source Beutler Lab
Gene Symbol Nphp4
Ensembl Gene ENSMUSG00000039577
Gene Name nephronophthisis 4 (juvenile) homolog (human)
Synonyms nmf192, 4930564O18Rik
MMRRC Submission 068907-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.142) question?
Stock # R9089 (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 152645673 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 1227 (V1227A)
Ref Sequence ENSEMBL: ENSMUSP00000049920 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056567] [ENSMUST00000081393]
AlphaFold P59240
Predicted Effect possibly damaging
Transcript: ENSMUST00000056567
AA Change: V1227A

PolyPhen 2 Score 0.870 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: V1227A

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 possibly damaging
Transcript: ENSMUST00000081393
AA Change: V1227A

PolyPhen 2 Score 0.870 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: V1227A

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: 99.8%
  • 20x: 99.3%
Validation Efficiency 100% (67/67)
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700122O11Rik T A 17: 48,347,951 (GRCm39) R118* probably null Het
Acadsb T C 7: 131,027,504 (GRCm39) V68A probably damaging Het
Adgb T C 10: 10,318,432 (GRCm39) R137G probably benign Het
Adgrl3 C A 5: 81,808,291 (GRCm39) N622K possibly damaging Het
Ager C A 17: 34,819,579 (GRCm39) P366T probably benign Het
Barx2 C A 9: 31,765,443 (GRCm39) W184L probably damaging Het
Bckdha A C 7: 25,341,144 (GRCm39) N72K probably benign Het
Blm A T 7: 80,162,867 (GRCm39) D161E probably damaging Het
Ccdc121rt2 A T 5: 112,598,757 (GRCm39) R435W probably damaging Het
Cd96 G T 16: 45,870,068 (GRCm39) T467N probably benign Het
Cdk13 A T 13: 17,978,444 (GRCm39) S265T unknown Het
Col6a5 A C 9: 105,766,142 (GRCm39) I1926S probably damaging Het
Csgalnact2 A T 6: 118,097,983 (GRCm39) V361D probably damaging Het
Cstf1 T A 2: 172,217,807 (GRCm39) M140K Het
Ddx41 A T 13: 55,683,424 (GRCm39) S128T probably benign Het
Deaf1 A T 7: 140,877,465 (GRCm39) V554D probably damaging Het
Dido1 C T 2: 180,303,293 (GRCm39) S1537N probably benign Het
Dmwd T C 7: 18,811,980 (GRCm39) S145P probably damaging Het
Eftud2 A G 11: 102,759,971 (GRCm39) S125P probably benign Het
Gga1 A G 15: 78,773,952 (GRCm39) D325G probably damaging Het
Gm43518 T C 5: 124,072,329 (GRCm39) probably null Het
Got1l1 A T 8: 27,690,889 (GRCm39) V53E probably damaging Het
Helz2 A T 2: 180,881,433 (GRCm39) C350S probably damaging Het
Ipo7 T A 7: 109,643,666 (GRCm39) F398I possibly damaging Het
Itga11 A G 9: 62,678,662 (GRCm39) N943S probably damaging Het
Itpa T A 2: 130,509,857 (GRCm39) probably null Het
Itpr3 G A 17: 27,337,651 (GRCm39) probably benign Het
Kbtbd4 A T 2: 90,737,909 (GRCm39) N220Y possibly damaging Het
Kdm5b T A 1: 134,535,506 (GRCm39) F594L probably damaging Het
Klhdc4 C T 8: 122,524,684 (GRCm39) V446I probably benign Het
Klk1b1 A G 7: 43,620,668 (GRCm39) I253V possibly damaging Het
Kynu T A 2: 43,489,620 (GRCm39) M135K probably damaging Het
Lgi1 T C 19: 38,294,095 (GRCm39) I289T possibly damaging Het
Lhx2 A G 2: 38,250,045 (GRCm39) N288S probably damaging Het
Lrp6 G C 6: 134,488,169 (GRCm39) A309G probably damaging Het
Map2 T A 1: 66,452,098 (GRCm39) N329K probably benign Het
Med15 G A 16: 17,473,421 (GRCm39) P476L unknown Het
Muc16 A T 9: 18,555,846 (GRCm39) N3482K unknown Het
Nemf A C 12: 69,400,628 (GRCm39) V149G probably damaging Het
Notch3 T C 17: 32,370,521 (GRCm39) S706G probably benign Het
Or1e31 A G 11: 73,690,052 (GRCm39) F177S probably damaging Het
Or2a52 A T 6: 43,144,917 (GRCm39) R308S probably benign Het
Or6c70 A G 10: 129,710,488 (GRCm39) L46P probably damaging Het
Parp2 A G 14: 51,052,327 (GRCm39) T102A probably damaging Het
Pcdhgc3 T C 18: 37,941,264 (GRCm39) V555A possibly damaging Het
Plk5 C G 10: 80,193,830 (GRCm39) R40G probably damaging Het
Ralgapa1 A C 12: 55,723,351 (GRCm39) L1725R probably damaging Het
Reln G T 5: 22,130,198 (GRCm39) D2704E probably benign Het
Sart3 C A 5: 113,891,756 (GRCm39) E405D possibly damaging Het
Scin A T 12: 40,131,703 (GRCm39) L277* probably null Het
Sec62 T A 3: 30,868,383 (GRCm39) V204E probably benign Het
Serpina3a T C 12: 104,085,956 (GRCm39) I137T possibly damaging Het
Sh3rf1 T C 8: 61,825,613 (GRCm39) M536T probably benign Het
Slc45a4 T C 15: 73,457,953 (GRCm39) H532R probably damaging Het
Svs5 A G 2: 164,079,341 (GRCm39) F189L probably benign Het
Synm T C 7: 67,408,766 (GRCm39) D204G probably damaging Het
Tmtc1 A T 6: 148,147,215 (GRCm39) H827Q possibly damaging Het
Tnfrsf25 T A 4: 152,201,929 (GRCm39) C135* probably null Het
Unc13b T G 4: 43,095,847 (GRCm39) I85S probably damaging Het
Ush2a T A 1: 188,487,374 (GRCm39) Y3047* probably null Het
Vmn1r75 T C 7: 11,614,453 (GRCm39) S62P probably damaging Het
Vps50 T C 6: 3,536,884 (GRCm39) V285A probably benign Het
Vwa5b1 T A 4: 138,296,742 (GRCm39) D1095V probably benign Het
Zdhhc21 T A 4: 82,725,292 (GRCm39) D208V probably damaging Het
Zfp422 A C 6: 116,604,086 (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
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
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'- TGCTCAAGAGAGTCCAGGCTAG -3'
(R):5'- TTGTGCAAACCTCCACCAGC -3'

Sequencing Primer
(F):5'- GCTCGCCCCAGTCCTATACATAG -3'
(R):5'- ACCTCCACCAGCTACTGTGG -3'
Posted On 2021-12-30