Incidental Mutation 'R9159:Nphp3'
ID 695589
Institutional Source Beutler Lab
Gene Symbol Nphp3
Ensembl Gene ENSMUSG00000032558
Gene Name nephronophthisis 3 (adolescent)
Synonyms pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9159 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 103879743-103921010 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 103897980 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 523 (L523Q)
Ref Sequence ENSEMBL: ENSMUSP00000035167 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035167] [ENSMUST00000193439] [ENSMUST00000194774]
AlphaFold Q7TNH6
Predicted Effect probably damaging
Transcript: ENSMUST00000035167
AA Change: L523Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: L523Q

DomainStartEndE-ValueType
low complexity region 46 69 N/A INTRINSIC
coiled coil region 107 203 N/A INTRINSIC
low complexity region 512 537 N/A INTRINSIC
low complexity region 613 627 N/A INTRINSIC
low complexity region 640 650 N/A INTRINSIC
TPR 938 971 3.16e1 SMART
TPR 980 1013 7.74e-2 SMART
TPR 1022 1055 3.24e1 SMART
low complexity region 1066 1080 N/A INTRINSIC
TPR 1088 1121 3.67e-3 SMART
TPR 1130 1163 1.3e-3 SMART
TPR 1172 1205 4.38e-1 SMART
TPR 1214 1247 8.69e-5 SMART
TPR 1256 1289 9.03e-3 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000193439
AA Change: L429Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141540
Gene: ENSMUSG00000032558
AA Change: L429Q

DomainStartEndE-ValueType
coiled coil region 75 109 N/A INTRINSIC
low complexity region 418 443 N/A INTRINSIC
low complexity region 519 532 N/A INTRINSIC
Predicted Effect
SMART Domains Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: L403Q

DomainStartEndE-ValueType
coiled coil region 49 83 N/A INTRINSIC
Pfam:NACHT 400 559 2e-6 PFAM
TPR 818 851 3.16e1 SMART
TPR 860 893 7.74e-2 SMART
TPR 902 935 3.24e1 SMART
low complexity region 946 960 N/A INTRINSIC
TPR 968 1001 3.67e-3 SMART
TPR 1010 1043 1.3e-3 SMART
TPR 1052 1085 4.38e-1 SMART
TPR 1094 1127 8.69e-5 SMART
TPR 1136 1169 9.03e-3 SMART
Meta Mutation Damage Score 0.6329 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.2%
Validation Efficiency 97% (72/74)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011]
PHENOTYPE: Homozygous hypomorphic mice display slowly progressing kidney cysts, enlarged kidneys, increased blood urea nitrogen, kidney inflammation and associated fibrosis, and premature death. Homozygous null mice display mid gestational lethality with partial penetrance of situs inversus. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9930012K11Rik A T 14: 70,394,238 (GRCm39) M179K probably benign Het
A030003K21Rik A G 1: 82,920,787 (GRCm39) V86A unknown Het
AC133488.1 A T 16: 18,440,075 (GRCm39) V363E probably benign Het
Adamts16 A G 13: 70,901,408 (GRCm39) S890P probably benign Het
Adgrf4 A G 17: 42,973,293 (GRCm39) V685A probably benign Het
Aff1 T A 5: 103,990,131 (GRCm39) M867K possibly damaging Het
Apba3 T A 10: 81,106,867 (GRCm39) S225T Het
Aplp1 T A 7: 30,141,775 (GRCm39) T228S probably benign Het
Arhgap18 A G 10: 26,730,886 (GRCm39) D188G probably benign Het
BC024063 T A 10: 81,944,906 (GRCm39) S175R possibly damaging Het
Bloc1s6 T G 2: 122,580,548 (GRCm39) S2R probably damaging Het
Cd209b A G 8: 3,974,245 (GRCm39) I119T possibly damaging Het
Cdk8 T C 5: 146,168,549 (GRCm39) V16A probably damaging Het
Cep295 A G 9: 15,252,904 (GRCm39) M308T probably benign Het
Cfap53 T A 18: 74,416,272 (GRCm39) Y2N probably damaging Het
Col28a1 T A 6: 8,014,993 (GRCm39) D804V probably damaging Het
Csta3 G A 16: 36,038,069 (GRCm39) V69I probably benign Het
Cyp2c40 A T 19: 39,762,317 (GRCm39) D443E probably damaging Het
Cyp2d9 A G 15: 82,338,572 (GRCm39) D202G possibly damaging Het
Dchs1 G A 7: 105,415,126 (GRCm39) A686V probably benign Het
Egf A T 3: 129,472,026 (GRCm39) N1199K probably benign Het
Eva1a A G 6: 82,068,855 (GRCm39) R61G possibly damaging Het
Exoc6 T A 19: 37,597,478 (GRCm39) D626E probably benign Het
Exosc10 T C 4: 148,663,916 (GRCm39) probably null Het
Firrm A G 1: 163,814,514 (GRCm39) I143T probably damaging Het
Gm12888 T C 4: 121,176,600 (GRCm39) Q67R probably null Het
Gm16485 A G 9: 8,972,319 (GRCm39) S62G unknown Het
Gng4 T C 13: 13,999,896 (GRCm39) I55T probably damaging Het
Gpihbp1 A G 15: 75,469,830 (GRCm39) S182G possibly damaging Het
Hax1 T C 3: 89,903,127 (GRCm39) R251G probably damaging Het
Igf2bp2 G A 16: 21,900,502 (GRCm39) T213I probably damaging Het
Il23a T A 10: 128,133,427 (GRCm39) K66* probably null Het
Itga2 A T 13: 115,014,298 (GRCm39) L210* probably null Het
Ltbp2 G A 12: 84,837,864 (GRCm39) P1192L probably benign Het
Matr3 T A 18: 35,712,355 (GRCm39) M389K possibly damaging Het
Mettl15 T C 2: 108,923,444 (GRCm39) D326G probably damaging Het
Mta1 T A 12: 113,100,025 (GRCm39) V645E probably damaging Het
Muc5ac T C 7: 141,363,529 (GRCm39) I2280T unknown Het
Naa15 T A 3: 51,358,802 (GRCm39) N362K probably benign Het
Necab2 T C 8: 120,189,303 (GRCm39) Y158H probably damaging Het
Nphs1 T G 7: 30,165,026 (GRCm39) F540V possibly damaging Het
Or2av9 A G 11: 58,381,350 (GRCm39) V77A probably damaging Het
Or2k2 A G 4: 58,785,320 (GRCm39) I134T probably benign Het
Or5p55 A T 7: 107,567,524 (GRCm39) R307* probably null Het
Ppa1 A T 10: 61,496,784 (GRCm39) I91F probably damaging Het
Prdm6 C A 18: 53,598,019 (GRCm39) A127D unknown Het
Prdm8 T C 5: 98,334,175 (GRCm39) F581L probably damaging Het
Rbbp6 T C 7: 122,589,428 (GRCm39) I372T probably damaging Het
Rnf144b A G 13: 47,396,348 (GRCm39) I228M probably damaging Het
Rsf1 CG CGACGGCGGGG 7: 97,229,115 (GRCm39) probably benign Het
Setd2 T C 9: 110,374,385 (GRCm39) probably null Het
Sez6l T C 5: 112,613,824 (GRCm39) H441R possibly damaging Het
Shbg G A 11: 69,506,430 (GRCm39) L327F probably benign Het
Sik3 C T 9: 46,123,539 (GRCm39) Q1113* probably null Het
Smad2 T A 18: 76,395,573 (GRCm39) I4N possibly damaging Het
Spata31h1 G A 10: 82,118,524 (GRCm39) R4829* probably null Het
Sult2b1 T A 7: 45,391,534 (GRCm39) E84V probably damaging Het
Tbc1d8 A G 1: 39,444,474 (GRCm39) Y162H Het
Tedc2 A G 17: 24,436,705 (GRCm39) L308P probably damaging Het
Tmc5 T C 7: 118,233,264 (GRCm39) V26A probably benign Het
Tmem120b T A 5: 123,242,566 (GRCm39) N181K possibly damaging Het
Tmem229b T G 12: 79,011,448 (GRCm39) N161T possibly damaging Het
Tmem43 A C 6: 91,459,291 (GRCm39) D254A probably benign Het
Trpv6 T C 6: 41,603,074 (GRCm39) D266G probably benign Het
Tspan9 A G 6: 127,943,717 (GRCm39) I102T possibly damaging Het
Ung A G 5: 114,270,166 (GRCm39) probably benign Het
Upp2 C T 2: 58,667,996 (GRCm39) H230Y probably damaging Het
Vmn1r184 G A 7: 25,966,545 (GRCm39) S97N possibly damaging Het
Vmn2r73 A T 7: 85,521,931 (GRCm39) V136E possibly damaging Het
Wdr20rt T C 12: 65,272,918 (GRCm39) V127A probably damaging Het
Yme1l1 T A 2: 23,063,058 (GRCm39) F210I probably damaging Het
Yrdc T C 4: 124,747,811 (GRCm39) probably null Het
Zfhx4 G T 3: 5,464,312 (GRCm39) R1515L probably damaging Het
Zfhx4 C T 3: 5,466,217 (GRCm39) P2150L probably damaging Het
Zfp267 C A 3: 36,219,902 (GRCm39) H642N possibly damaging Het
Zfp988 C T 4: 147,416,450 (GRCm39) P295S possibly damaging Het
Other mutations in Nphp3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01707:Nphp3 APN 9 103,895,357 (GRCm39) missense possibly damaging 0.75
IGL02329:Nphp3 APN 9 103,903,167 (GRCm39) missense probably benign 0.19
lithograph UTSW 9 103,919,189 (GRCm39) missense probably damaging 1.00
quartzite UTSW 9 103,913,376 (GRCm39) missense probably damaging 1.00
F5770:Nphp3 UTSW 9 103,913,093 (GRCm39) critical splice donor site probably null
FR4548:Nphp3 UTSW 9 103,903,138 (GRCm39) small deletion probably benign
FR4589:Nphp3 UTSW 9 103,903,138 (GRCm39) small deletion probably benign
R0112:Nphp3 UTSW 9 103,914,547 (GRCm39) missense possibly damaging 0.80
R0555:Nphp3 UTSW 9 103,900,633 (GRCm39) missense probably damaging 1.00
R0632:Nphp3 UTSW 9 103,895,473 (GRCm39) missense probably damaging 1.00
R0674:Nphp3 UTSW 9 103,913,481 (GRCm39) critical splice donor site probably null
R0743:Nphp3 UTSW 9 103,899,967 (GRCm39) small deletion probably benign
R0853:Nphp3 UTSW 9 103,909,132 (GRCm39) missense probably benign 0.03
R0920:Nphp3 UTSW 9 103,909,106 (GRCm39) missense probably benign 0.00
R1420:Nphp3 UTSW 9 103,913,092 (GRCm39) critical splice donor site probably null
R1464:Nphp3 UTSW 9 103,909,078 (GRCm39) splice site probably benign
R1476:Nphp3 UTSW 9 103,903,126 (GRCm39) missense possibly damaging 0.81
R1585:Nphp3 UTSW 9 103,886,413 (GRCm39) missense probably damaging 1.00
R1608:Nphp3 UTSW 9 103,913,039 (GRCm39) missense probably benign 0.30
R1688:Nphp3 UTSW 9 103,880,323 (GRCm39) missense probably damaging 1.00
R1691:Nphp3 UTSW 9 103,880,010 (GRCm39) missense probably benign
R1807:Nphp3 UTSW 9 103,897,940 (GRCm39) missense probably benign 0.01
R1857:Nphp3 UTSW 9 103,898,493 (GRCm39) missense possibly damaging 0.87
R1962:Nphp3 UTSW 9 103,898,537 (GRCm39) missense probably benign 0.00
R2127:Nphp3 UTSW 9 103,885,442 (GRCm39) missense probably damaging 0.98
R2138:Nphp3 UTSW 9 103,903,102 (GRCm39) missense possibly damaging 0.89
R2233:Nphp3 UTSW 9 103,914,575 (GRCm39) missense probably benign 0.02
R2234:Nphp3 UTSW 9 103,914,575 (GRCm39) missense probably benign 0.02
R3861:Nphp3 UTSW 9 103,916,525 (GRCm39) unclassified probably benign
R3928:Nphp3 UTSW 9 103,888,929 (GRCm39) missense probably damaging 0.99
R3961:Nphp3 UTSW 9 103,880,241 (GRCm39) nonsense probably null
R4182:Nphp3 UTSW 9 103,915,663 (GRCm39) missense probably benign 0.06
R4294:Nphp3 UTSW 9 103,899,916 (GRCm39) missense probably damaging 1.00
R4387:Nphp3 UTSW 9 103,907,219 (GRCm39) missense possibly damaging 0.94
R4625:Nphp3 UTSW 9 103,913,358 (GRCm39) missense possibly damaging 0.66
R4628:Nphp3 UTSW 9 103,880,257 (GRCm39) missense probably damaging 0.99
R4696:Nphp3 UTSW 9 103,899,931 (GRCm39) missense probably benign 0.01
R4865:Nphp3 UTSW 9 103,909,169 (GRCm39) missense probably benign
R4886:Nphp3 UTSW 9 103,880,193 (GRCm39) missense probably damaging 1.00
R4973:Nphp3 UTSW 9 103,909,198 (GRCm39) missense probably benign
R5445:Nphp3 UTSW 9 103,881,922 (GRCm39) missense probably damaging 1.00
R5451:Nphp3 UTSW 9 103,919,221 (GRCm39) missense probably benign
R5520:Nphp3 UTSW 9 103,901,872 (GRCm39) missense probably benign 0.30
R5641:Nphp3 UTSW 9 103,913,352 (GRCm39) missense probably damaging 1.00
R5847:Nphp3 UTSW 9 103,880,236 (GRCm39) missense probably damaging 1.00
R5928:Nphp3 UTSW 9 103,912,996 (GRCm39) missense probably benign 0.01
R5931:Nphp3 UTSW 9 103,897,945 (GRCm39) missense probably damaging 1.00
R6161:Nphp3 UTSW 9 103,909,105 (GRCm39) missense probably benign 0.11
R6298:Nphp3 UTSW 9 103,892,640 (GRCm39) missense probably damaging 1.00
R6890:Nphp3 UTSW 9 103,919,153 (GRCm39) missense probably damaging 0.96
R7009:Nphp3 UTSW 9 103,893,315 (GRCm39) missense probably null 0.00
R7065:Nphp3 UTSW 9 103,919,189 (GRCm39) missense probably damaging 1.00
R7146:Nphp3 UTSW 9 103,882,036 (GRCm39) nonsense probably null
R7198:Nphp3 UTSW 9 103,881,974 (GRCm39) missense probably damaging 1.00
R7360:Nphp3 UTSW 9 103,893,277 (GRCm39) critical splice acceptor site probably null
R7369:Nphp3 UTSW 9 103,895,449 (GRCm39) missense probably damaging 0.99
R7554:Nphp3 UTSW 9 103,919,270 (GRCm39) missense probably damaging 0.98
R7591:Nphp3 UTSW 9 103,895,477 (GRCm39) critical splice donor site probably null
R7665:Nphp3 UTSW 9 103,882,592 (GRCm39) splice site probably null
R7672:Nphp3 UTSW 9 103,909,159 (GRCm39) missense probably benign
R7675:Nphp3 UTSW 9 103,893,287 (GRCm39) missense probably benign
R8039:Nphp3 UTSW 9 103,909,162 (GRCm39) missense probably benign
R8145:Nphp3 UTSW 9 103,913,050 (GRCm39) missense probably benign 0.16
R8211:Nphp3 UTSW 9 103,909,096 (GRCm39) missense possibly damaging 0.80
R8882:Nphp3 UTSW 9 103,882,793 (GRCm39) missense possibly damaging 0.77
R9020:Nphp3 UTSW 9 103,909,150 (GRCm39) missense probably benign 0.00
R9132:Nphp3 UTSW 9 103,897,980 (GRCm39) missense probably damaging 1.00
R9135:Nphp3 UTSW 9 103,909,214 (GRCm39) missense probably damaging 0.99
R9204:Nphp3 UTSW 9 103,919,305 (GRCm39) missense probably benign
R9226:Nphp3 UTSW 9 103,885,328 (GRCm39) missense probably benign 0.00
R9229:Nphp3 UTSW 9 103,913,376 (GRCm39) missense probably damaging 1.00
R9526:Nphp3 UTSW 9 103,913,337 (GRCm39) missense probably damaging 1.00
R9678:Nphp3 UTSW 9 103,900,686 (GRCm39) missense possibly damaging 0.90
R9731:Nphp3 UTSW 9 103,886,369 (GRCm39) missense probably damaging 1.00
V7583:Nphp3 UTSW 9 103,913,093 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- AGGCTCCAGTGTACAGATCAG -3'
(R):5'- ACATTCAACTAAGAGCATGCAG -3'

Sequencing Primer
(F):5'- CGGCCAGATGCAAGTTTTTC -3'
(R):5'- GGTCATCTTTAGTTACACAGCGAG -3'
Posted On 2022-01-20