Incidental Mutation 'R1857:Nphp3'
ID 206245
Institutional Source Beutler Lab
Gene Symbol Nphp3
Ensembl Gene ENSMUSG00000032558
Gene Name nephronophthisis 3 (adolescent)
Synonyms pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3
MMRRC Submission 039881-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1857 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 103879743-103921010 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 103898493 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 432 (I432T)
Ref Sequence ENSEMBL: ENSMUSP00000141596 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035167] [ENSMUST00000193439] [ENSMUST00000194774]
AlphaFold Q7TNH6
Predicted Effect possibly damaging
Transcript: ENSMUST00000035167
AA Change: I552T

PolyPhen 2 Score 0.679 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: I552T

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
SMART Domains Protein: ENSMUSP00000116459
Gene: ENSMUSG00000032558
AA Change: I432T

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 noncoding transcript
Transcript: ENSMUST00000191919
Predicted Effect possibly damaging
Transcript: ENSMUST00000193439
AA Change: I458T

PolyPhen 2 Score 0.785 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000141540
Gene: ENSMUSG00000032558
AA Change: I458T

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 noncoding transcript
Transcript: ENSMUST00000193642
Predicted Effect possibly damaging
Transcript: ENSMUST00000194774
AA Change: I432T

PolyPhen 2 Score 0.870 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: I432T

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
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.9%
  • 10x: 95.3%
  • 20x: 92.2%
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 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: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aars1 T A 8: 111,766,789 (GRCm39) I57N probably damaging Het
Abca15 T C 7: 119,960,592 (GRCm39) S685P probably damaging Het
Adpgk G T 9: 59,222,248 (GRCm39) V392L probably benign Het
Akap14 C T X: 36,420,779 (GRCm39) A476T probably damaging Het
Amdhd1 A T 10: 93,367,416 (GRCm39) I246N probably damaging Het
Amhr2 T A 15: 102,355,212 (GRCm39) L165* probably null Het
Atr T A 9: 95,747,150 (GRCm39) I144N probably damaging Het
Ccdc33 T C 9: 57,939,991 (GRCm39) N750S possibly damaging Het
Cdh23 A G 10: 60,159,076 (GRCm39) I2233T probably damaging Het
Cfap46 C A 7: 139,233,324 (GRCm39) V774F probably damaging Het
Cfap69 G T 5: 5,632,518 (GRCm39) T362K possibly damaging Het
Cnih3 A G 1: 181,277,638 (GRCm39) H101R probably damaging Het
Crebrf T A 17: 26,961,937 (GRCm39) Y345N probably benign Het
Cyb5r4 C T 9: 86,923,332 (GRCm39) S185L probably benign Het
Cyp2j5 T C 4: 96,547,723 (GRCm39) E173G possibly damaging Het
Cyp3a41b T A 5: 145,503,660 (GRCm39) I296F probably benign Het
Dse T C 10: 34,029,225 (GRCm39) T622A probably benign Het
Duxf4 A G 10: 58,071,602 (GRCm39) V204A probably benign Het
Dync1h1 T A 12: 110,629,059 (GRCm39) F4205L probably damaging Het
Eif3a A C 19: 60,770,635 (GRCm39) L71V probably damaging Het
Eif3h T C 15: 51,662,674 (GRCm39) Y124C probably damaging Het
Eif4g3 A T 4: 137,903,187 (GRCm39) Q1169L possibly damaging Het
Endod1 T A 9: 14,268,405 (GRCm39) H360L probably benign Het
Fbxo38 A G 18: 62,648,489 (GRCm39) I683T probably damaging Het
Frem2 T A 3: 53,562,294 (GRCm39) T738S probably benign Het
Gm1527 A T 3: 28,957,539 (GRCm39) T148S probably damaging Het
Gm4894 T C 9: 49,189,976 (GRCm39) S84P unknown Het
Hsh2d G A 8: 72,954,304 (GRCm39) D229N probably benign Het
Il1f10 A T 2: 24,182,817 (GRCm39) D31V possibly damaging Het
Lrrc56 A G 7: 140,787,421 (GRCm39) M353V probably benign Het
Meiob T C 17: 25,042,544 (GRCm39) V124A probably damaging Het
Mmp11 A T 10: 75,764,191 (GRCm39) D91E probably benign Het
Mpped2 T C 2: 106,613,989 (GRCm39) Y108H probably damaging Het
Mroh9 A G 1: 162,866,714 (GRCm39) V674A probably damaging Het
Mtor G T 4: 148,565,336 (GRCm39) Q1015H probably damaging Het
Mylk3 G A 8: 86,055,223 (GRCm39) T711I probably damaging Het
Ndufaf6 G T 4: 11,053,474 (GRCm39) H277Q probably benign Het
Neurl4 G T 11: 69,796,361 (GRCm39) G435V probably damaging Het
Nipal2 A G 15: 34,678,779 (GRCm39) S21P possibly damaging Het
Nphp1 T A 2: 127,612,296 (GRCm39) D217V probably benign Het
Oprd1 T G 4: 131,840,992 (GRCm39) D322A probably damaging Het
Or10ag2 T C 2: 87,248,992 (GRCm39) L198P probably damaging Het
Or2b28 A G 13: 21,531,346 (GRCm39) M83V possibly damaging Het
Or56a3b T G 7: 104,770,751 (GRCm39) L29R probably benign Het
Pcdh10 C A 3: 45,334,372 (GRCm39) Q229K possibly damaging Het
Pdlim7 G A 13: 55,653,858 (GRCm39) T253M probably damaging Het
Pfdn1 C A 18: 36,584,153 (GRCm39) M60I probably benign Het
Pigc T G 1: 161,798,446 (GRCm39) S143A possibly damaging Het
Pkd1l2 T C 8: 117,767,408 (GRCm39) D1294G possibly damaging Het
Ppp2r1a T C 17: 21,181,951 (GRCm39) S490P possibly damaging Het
Ppp2r3d T A 9: 101,090,092 (GRCm39) N77I probably damaging Het
Pramel17 T C 4: 101,692,770 (GRCm39) Y410C probably damaging Het
Pramel29 C T 4: 143,935,091 (GRCm39) V217I possibly damaging Het
Prl7a2 A T 13: 27,843,163 (GRCm39) C213* probably null Het
Prpf8 T A 11: 75,386,249 (GRCm39) probably null Het
Psmd7 A T 8: 108,311,525 (GRCm39) N109K probably damaging Het
Ptprn T C 1: 75,224,549 (GRCm39) K936E possibly damaging Het
Ro60 T C 1: 143,646,488 (GRCm39) T86A probably benign Het
Ror1 A T 4: 100,298,700 (GRCm39) Q691L probably damaging Het
Sars2 A G 7: 28,449,437 (GRCm39) M322V probably benign Het
Scfd2 C A 5: 74,372,962 (GRCm39) E638* probably null Het
Scgb3a2 A G 18: 43,899,900 (GRCm39) T63A probably benign Het
Slc5a4a T C 10: 76,002,569 (GRCm39) S242P probably benign Het
Smarcd1 A G 15: 99,607,295 (GRCm39) K382E probably damaging Het
Sox5 T A 6: 143,906,541 (GRCm39) S305C probably damaging Het
Sp5 C A 2: 70,307,213 (GRCm39) H299Q possibly damaging Het
Stard13 T C 5: 151,018,903 (GRCm39) Y60C probably damaging Het
Tmprss6 A G 15: 78,336,752 (GRCm39) F383L probably damaging Het
Ttc23 T C 7: 67,328,821 (GRCm39) probably null Het
Ugt2b34 T C 5: 87,052,241 (GRCm39) T252A possibly damaging Het
Vangl2 A T 1: 171,837,464 (GRCm39) L115Q probably damaging Het
Vmn1r42 A G 6: 89,821,597 (GRCm39) I324T probably benign Het
Vwa5b1 A G 4: 138,296,413 (GRCm39) F1205L probably damaging Het
Zfp951 G C 5: 104,962,723 (GRCm39) T281R probably damaging Het
Zscan30 A G 18: 24,104,524 (GRCm39) noncoding transcript 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
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
R9159:Nphp3 UTSW 9 103,897,980 (GRCm39) missense probably damaging 1.00
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'- TTGTTGCAATGTGACTAGCCATG -3'
(R):5'- GGCTCCAGTGGTCAATCTTCAC -3'

Sequencing Primer
(F):5'- CTAGCCATGTAATTAAGGACTCCGG -3'
(R):5'- CAGAATTTGGGCAGTTCAGATTTC -3'
Posted On 2014-06-23