Incidental Mutation 'R7006:Nphp4'
ID 544712
Institutional Source Beutler Lab
Gene Symbol Nphp4
Ensembl Gene ENSMUSG00000039577
Gene Name nephronophthisis 4 (juvenile) homolog (human)
Synonyms nmf192, 4930564O18Rik
MMRRC Submission 045011-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.142) question?
Stock # R7006 (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 152573259 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 66 (T66A)
Ref Sequence ENSEMBL: ENSMUSP00000080128 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056567] [ENSMUST00000081393]
AlphaFold P59240
Predicted Effect probably benign
Transcript: ENSMUST00000056567
AA Change: T66A

PolyPhen 2 Score 0.124 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: T66A

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: T66A

PolyPhen 2 Score 0.124 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: T66A

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: 99.0%
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
AAdacl4fm3 A G 4: 144,447,853 (GRCm39) V41A probably benign Het
Adcy2 G A 13: 69,036,139 (GRCm39) T174M probably damaging Het
Ankfy1 T A 11: 72,631,290 (GRCm39) I412N probably benign Het
AW146154 T C 7: 41,130,648 (GRCm39) E156G possibly damaging Het
B4galnt1 T C 10: 127,005,700 (GRCm39) L267P probably benign Het
Bod1l T C 5: 41,989,895 (GRCm39) E276G probably damaging Het
Ccdc187 T C 2: 26,171,102 (GRCm39) T459A probably benign Het
Ccdc196 T A 12: 78,255,702 (GRCm39) *177R probably null Het
Cep72 G A 13: 74,198,427 (GRCm39) Q311* probably null Het
Cir1 T C 2: 73,140,834 (GRCm39) Q45R probably damaging Het
Ciz1 T C 2: 32,261,127 (GRCm39) probably null Het
Crtap G T 9: 114,215,391 (GRCm39) A166E probably damaging Het
Dipk1a A G 5: 108,058,027 (GRCm39) V132A probably benign Het
Dmp1 A G 5: 104,360,188 (GRCm39) D288G probably benign Het
Fhad1 CGG CG 4: 141,645,602 (GRCm39) probably null Het
Fmnl2 C A 2: 52,998,266 (GRCm39) Q544K probably benign Het
Gpsm1 T C 2: 26,212,572 (GRCm39) L72P probably damaging Het
Gys1 G A 7: 45,089,437 (GRCm39) A199T probably damaging Het
Kcnq3 A C 15: 65,892,165 (GRCm39) Y403* probably null Het
Kcp A C 6: 29,499,169 (GRCm39) Y298D probably damaging Het
Kif5c T C 2: 49,625,526 (GRCm39) S599P probably damaging Het
Krt20 A T 11: 99,328,587 (GRCm39) Y113N probably benign Het
Mcm8 T G 2: 132,665,181 (GRCm39) V191G probably damaging Het
Msr1 T A 8: 40,042,423 (GRCm39) D384V probably damaging Het
Mtpap A C 18: 4,380,873 (GRCm39) S184R possibly damaging Het
Npc1l1 G A 11: 6,167,731 (GRCm39) T1020M probably benign Het
Or1o3 T A 17: 37,573,625 (GRCm39) *310L probably null Het
Or4f14 C A 2: 111,742,601 (GRCm39) V225L probably benign Het
Or8h10 G A 2: 86,808,303 (GRCm39) T279I probably damaging Het
Or8k18 T A 2: 86,085,572 (GRCm39) Q155L probably benign Het
Phf11d G T 14: 59,590,823 (GRCm39) T178K probably benign Het
Ppm1d A G 11: 85,227,977 (GRCm39) K298E possibly damaging Het
Rab2b A T 14: 52,503,690 (GRCm39) I144K probably benign Het
Stoml1 A G 9: 58,167,523 (GRCm39) D5G probably damaging Het
Styxl2 T C 1: 165,926,663 (GRCm39) N983S probably benign Het
Tanc1 T C 2: 59,626,188 (GRCm39) V515A probably damaging Het
Tas1r3 A G 4: 155,947,361 (GRCm39) V108A possibly damaging Het
Tifab T C 13: 56,324,059 (GRCm39) Y128C probably benign Het
Tmc6 G T 11: 117,665,083 (GRCm39) R397S probably damaging Het
Tnpo3 C T 6: 29,589,162 (GRCm39) A63T probably damaging Het
Trgc4 T A 13: 19,528,995 (GRCm39) probably benign Het
Usp16 G T 16: 87,268,724 (GRCm39) C284F probably damaging Het
Wipf1 T C 2: 73,267,441 (GRCm39) D319G probably damaging Het
Xpnpep3 T A 15: 81,326,649 (GRCm39) W347R probably damaging Het
Zfp180 G T 7: 23,804,537 (GRCm39) E319* probably null 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
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
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'- GTCACAAGGAAGTTGAGTTGCC -3'
(R):5'- GGAAACAGAGTGTCCCACTAC -3'

Sequencing Primer
(F):5'- AAGTTGAGTTGCCAGTAGCTGAATG -3'
(R):5'- GTGTCCCACTACTAAGACAAGCTTG -3'
Posted On 2019-05-13