Incidental Mutation 'R1476:Nphp3'
ID 164081
Institutional Source Beutler Lab
Gene Symbol Nphp3
Ensembl Gene ENSMUSG00000032558
Gene Name nephronophthisis 3 (adolescent)
Synonyms pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3
MMRRC Submission 039529-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1476 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 103879743-103921010 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 103903126 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Leucine at position 701 (R701L)
Ref Sequence ENSEMBL: ENSMUSP00000035167 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035167] [ENSMUST00000193439] [ENSMUST00000194774]
AlphaFold Q7TNH6
Predicted Effect possibly damaging
Transcript: ENSMUST00000035167
AA Change: R701L

PolyPhen 2 Score 0.805 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: R701L

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 unknown
Transcript: ENSMUST00000129819
AA Change: R581L
SMART Domains Protein: ENSMUSP00000116459
Gene: ENSMUSG00000032558
AA Change: R581L

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 probably benign
Transcript: ENSMUST00000193439
SMART Domains Protein: ENSMUSP00000141540
Gene: ENSMUSG00000032558

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 unknown
Transcript: ENSMUST00000194774
AA Change: R581L
SMART Domains Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: R581L

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 0.1046 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.1%
Validation Efficiency 95% (80/84)
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: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310033P09Rik A G 11: 59,099,528 (GRCm39) probably benign Het
A730015C16Rik G A 4: 108,705,205 (GRCm39) V40M probably damaging Het
Abcg2 A G 6: 58,655,322 (GRCm39) D419G probably benign Het
Adamts17 A C 7: 66,725,091 (GRCm39) E777A probably damaging Het
Ak1 A G 2: 32,523,478 (GRCm39) K166R probably benign Het
Ankrd12 T C 17: 66,293,300 (GRCm39) K711R probably damaging Het
Ate1 A T 7: 130,020,301 (GRCm39) probably null Het
Atp5f1a A G 18: 77,869,625 (GRCm39) H519R probably benign Het
Best1 G T 19: 9,967,853 (GRCm39) Y284* probably null Het
C2cd6 A G 1: 59,115,887 (GRCm39) probably benign Het
Casz1 G T 4: 149,030,628 (GRCm39) V1216L probably benign Het
Cdc42bpg A G 19: 6,363,812 (GRCm39) D493G probably damaging Het
Ces2f A G 8: 105,679,134 (GRCm39) D317G possibly damaging Het
Chst15 A T 7: 131,872,002 (GRCm39) M93K possibly damaging Het
Cntnap5a T C 1: 115,828,750 (GRCm39) L58P probably damaging Het
Crip3 T C 17: 46,741,702 (GRCm39) probably benign Het
Csmd2 G A 4: 128,380,794 (GRCm39) E2117K probably benign Het
Cstf3 A G 2: 104,478,564 (GRCm39) D212G possibly damaging Het
Cttnbp2 T C 6: 18,434,220 (GRCm39) K546R probably damaging Het
Cubn A G 2: 13,480,931 (GRCm39) I308T probably benign Het
Cxcl9 T A 5: 92,472,972 (GRCm39) D75V probably damaging Het
Dcdc5 C T 2: 106,188,977 (GRCm39) noncoding transcript Het
Defa30 C A 8: 21,624,752 (GRCm39) T25K possibly damaging Het
Dock7 A T 4: 98,967,672 (GRCm39) H239Q possibly damaging Het
Dpp4 A G 2: 62,178,245 (GRCm39) V629A possibly damaging Het
Fam83a T C 15: 57,873,341 (GRCm39) M390T probably benign Het
Fem1c A G 18: 46,657,552 (GRCm39) L54P probably damaging Het
Fntb T A 12: 76,957,007 (GRCm39) M282K probably benign Het
Galnt2l A G 8: 122,996,323 (GRCm39) probably benign Het
Gm11099 G A 2: 58,749,482 (GRCm39) probably benign Het
Gm1527 T C 3: 28,980,705 (GRCm39) S602P probably benign Het
Gm5478 T A 15: 101,553,080 (GRCm39) I331F probably damaging Het
Gm7853 C A 14: 35,811,540 (GRCm39) noncoding transcript Het
Gsta2 A T 9: 78,249,147 (GRCm39) C18S probably benign Het
H1f8 T C 6: 115,924,701 (GRCm39) V69A possibly damaging Het
Hecw1 T C 13: 14,480,671 (GRCm39) E465G probably damaging Het
Herc1 A G 9: 66,415,548 (GRCm39) D4841G probably damaging Het
Hus1b A G 13: 31,130,984 (GRCm39) V225A probably benign Het
Keg1 A T 19: 12,693,387 (GRCm39) M137L probably benign Het
Kmt2a C T 9: 44,735,932 (GRCm39) probably benign Het
Megf6 G T 4: 154,261,578 (GRCm39) V68L probably benign Het
Mga T A 2: 119,772,156 (GRCm39) V1672E probably damaging Het
Mios T C 6: 8,234,237 (GRCm39) S803P probably benign Het
Mrtfa T C 15: 80,902,409 (GRCm39) probably benign Het
Msh4 A T 3: 153,569,021 (GRCm39) Y851N probably damaging Het
Mybl1 A C 1: 9,742,886 (GRCm39) probably null Het
Myo5c A G 9: 75,183,221 (GRCm39) Y865C probably damaging Het
Naip1 T C 13: 100,563,378 (GRCm39) S596G probably benign Het
Nek5 G T 8: 22,586,747 (GRCm39) Q355K possibly damaging Het
Or52n2 A T 7: 104,542,444 (GRCm39) Y130* probably null Het
Or5j3 T C 2: 86,128,823 (GRCm39) I221T probably damaging Het
Or5m10 T A 2: 85,717,592 (GRCm39) Y149* probably null Het
Or5t9 T C 2: 86,659,542 (GRCm39) S149P probably benign Het
Or9g4 T A 2: 85,505,262 (GRCm39) T78S possibly damaging Het
Palm A G 10: 79,651,021 (GRCm39) N149D possibly damaging Het
Pot1b T C 17: 55,960,451 (GRCm39) I626M possibly damaging Het
Ptprt T A 2: 161,769,404 (GRCm39) D487V probably damaging Het
Qpct A G 17: 79,378,201 (GRCm39) I124V probably benign Het
Rbm12b1 T A 4: 12,145,817 (GRCm39) D596E possibly damaging Het
Rnf157 A G 11: 116,245,585 (GRCm39) C277R probably damaging Het
Rnf169 A G 7: 99,574,535 (GRCm39) S687P possibly damaging Het
Sfxn1 T A 13: 54,246,469 (GRCm39) probably null Het
Slc6a21 T C 7: 44,922,052 (GRCm39) V649A probably benign Het
Slit3 A T 11: 35,577,126 (GRCm39) T1120S probably damaging Het
Spem2 A T 11: 69,708,896 (GRCm39) M58K probably benign Het
Sprr2k T A 3: 92,340,703 (GRCm39) probably benign Het
Sspo T C 6: 48,440,334 (GRCm39) probably null Het
Sv2b A T 7: 74,769,791 (GRCm39) F584I possibly damaging Het
Tkfc A T 19: 10,572,690 (GRCm39) M317K probably null Het
Tnni3k C T 3: 154,735,942 (GRCm39) G134S probably benign Het
Ttn C T 2: 76,570,124 (GRCm39) R26923H probably damaging Het
Tuba3b T C 6: 145,564,179 (GRCm39) V75A possibly damaging Het
Unc79 T C 12: 103,149,784 (GRCm39) L2626P probably damaging Het
Usp24 A T 4: 106,219,130 (GRCm39) I491F probably damaging Het
V1ra8 A T 6: 90,180,132 (GRCm39) I112F probably damaging Het
Vmn1r29 T G 6: 58,284,663 (GRCm39) F128V probably benign Het
Wdr87-ps A G 7: 29,234,315 (GRCm39) noncoding transcript Het
Zfp157 T A 5: 138,453,357 (GRCm39) probably null 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
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
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'- CTTCCCTTCTGCAACTGGAAGTCTG -3'
(R):5'- TTCAGCAGTGAGCCACATTCTCC -3'

Sequencing Primer
(F):5'- GCCATAGCCAGGCACCC -3'
(R):5'- GAACTCTGAGACCTGTTAAACTGG -3'
Posted On 2014-03-28