Incidental Mutation 'R7009:Nphp3'
ID 544909
Institutional Source Beutler Lab
Gene Symbol Nphp3
Ensembl Gene ENSMUSG00000032558
Gene Name nephronophthisis 3 (adolescent)
Synonyms pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3
MMRRC Submission 045111-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7009 (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 G at 103893315 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Glycine at position 434 (C434G)
Ref Sequence ENSEMBL: ENSMUSP00000035167 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035167] [ENSMUST00000193439] [ENSMUST00000194774]
AlphaFold Q7TNH6
Predicted Effect probably null
Transcript: ENSMUST00000035167
AA Change: C434G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: C434G

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 benign
Transcript: ENSMUST00000193439
AA Change: C340G

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000141540
Gene: ENSMUSG00000032558
AA Change: C340G

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 null
Transcript: ENSMUST00000194774
AA Change: C314G
SMART Domains Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: C314G

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: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.2%
Validation Efficiency 99% (82/83)
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: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921517D22Rik G T 13: 59,838,624 (GRCm39) D69E possibly damaging Het
Abat A C 16: 8,420,231 (GRCm39) M177L probably benign Het
Acadvl A G 11: 69,905,617 (GRCm39) probably null Het
Adam5 T C 8: 25,296,454 (GRCm39) N331S probably benign Het
Ager A G 17: 34,819,710 (GRCm39) E372G probably damaging Het
Angpt1 T A 15: 42,386,991 (GRCm39) Q121L possibly damaging Het
Apoa4 A T 9: 46,154,178 (GRCm39) I260F possibly damaging Het
Arhgap32 A T 9: 32,157,272 (GRCm39) I90F probably damaging Het
Arhgap5 A T 12: 52,566,422 (GRCm39) Q1131L probably benign Het
Bach1 G A 16: 87,516,179 (GRCm39) R240Q probably benign Het
Cacna2d3 A T 14: 28,691,322 (GRCm39) M1K probably null Het
Ccdc18 G A 5: 108,321,728 (GRCm39) probably null Het
Ccdc42 T C 11: 68,485,442 (GRCm39) F267S probably damaging Het
Cdh23 T A 10: 60,173,085 (GRCm39) Y1700F probably damaging Het
Cenpe A T 3: 134,940,962 (GRCm39) S704C probably damaging Het
Cenpe G A 3: 134,940,963 (GRCm39) S704N probably benign Het
Cfap299 A T 5: 98,932,379 (GRCm39) D193V probably damaging Het
Cfap54 A T 10: 92,710,881 (GRCm39) S2727T unknown Het
Clu T A 14: 66,209,281 (GRCm39) V113D probably damaging Het
Cnbd2 A G 2: 156,161,954 (GRCm39) I98V probably benign Het
Copa G T 1: 171,918,567 (GRCm39) R97L probably damaging Het
Epb41l1 C A 2: 156,376,603 (GRCm39) probably null Het
Etnk1 T A 6: 143,148,880 (GRCm39) probably null Het
Fnip1 A T 11: 54,393,761 (GRCm39) K732N probably damaging Het
G6pd2 A G 5: 61,966,234 (GRCm39) E3G probably benign Het
Gal3st2 A G 1: 93,801,481 (GRCm39) T95A probably benign Het
Gapvd1 A G 2: 34,590,829 (GRCm39) S948P probably damaging Het
Ggps1 A T 13: 14,228,750 (GRCm39) Y8* probably null Het
Gria2 T C 3: 80,614,279 (GRCm39) E587G probably damaging Het
Hpse T C 5: 100,840,145 (GRCm39) E324G probably benign Het
Il16 G A 7: 83,295,596 (GRCm39) T493I probably benign Het
Ints1 T C 5: 139,754,217 (GRCm39) T652A possibly damaging Het
Ism1 A G 2: 139,599,199 (GRCm39) I391V probably damaging Het
Katnb1 A G 8: 95,825,012 (GRCm39) D598G probably damaging Het
Kif5c A G 2: 49,647,441 (GRCm39) S880G probably benign Het
Klra8 T C 6: 130,102,147 (GRCm39) N96S probably benign Het
Krt79 T A 15: 101,839,876 (GRCm39) D373V probably damaging Het
Lamtor4 G A 5: 138,257,374 (GRCm39) R92Q probably benign Het
Lce1d C A 3: 92,593,353 (GRCm39) C20F unknown Het
Limk1 T C 5: 134,701,553 (GRCm39) T117A probably benign Het
Medag A T 5: 149,350,708 (GRCm39) K61M probably benign Het
Mkrn3 T C 7: 62,069,366 (GRCm39) M142V probably benign Het
Mob3c G A 4: 115,688,779 (GRCm39) R104H probably benign Het
Morc1 G T 16: 48,447,433 (GRCm39) R903L possibly damaging Het
Myh6 T C 14: 55,189,749 (GRCm39) E1099G probably damaging Het
Npr3 C T 15: 11,905,334 (GRCm39) C131Y probably damaging Het
Oacyl C A 18: 65,855,609 (GRCm39) Y112* probably null Het
Oprl1 A G 2: 181,360,174 (GRCm39) T77A probably damaging Het
Osgep A G 14: 51,162,165 (GRCm39) V24A probably damaging Het
Otx2 T A 14: 48,896,254 (GRCm39) K260M probably damaging Het
Pdcd11 T C 19: 47,101,581 (GRCm39) L922P probably benign Het
Pgap4 A T 4: 49,586,325 (GRCm39) M281K probably benign Het
Phldb1 A G 9: 44,605,705 (GRCm39) V375A probably damaging Het
Pip5k1b C T 19: 24,337,299 (GRCm39) probably null Het
Psmd3 G A 11: 98,573,592 (GRCm39) D13N probably benign Het
Ptprc G A 1: 137,992,291 (GRCm39) H1140Y probably damaging Het
Ranbp3l A T 15: 9,063,064 (GRCm39) H291L probably damaging Het
Rasa4 T A 5: 136,130,217 (GRCm39) D324E probably damaging Het
Rilpl1 T A 5: 124,641,755 (GRCm39) silent Het
Rin2 A C 2: 145,725,395 (GRCm39) D794A probably damaging Het
Ripk1 A G 13: 34,214,045 (GRCm39) I522M probably damaging Het
Rnf31 T C 14: 55,830,008 (GRCm39) Y143H probably benign Het
Rp1 T G 1: 4,112,291 (GRCm39) I1187L unknown Het
Rps6ka5 G A 12: 100,585,796 (GRCm39) H166Y probably damaging Het
Rrm1 T C 7: 102,109,541 (GRCm39) V455A probably damaging Het
Runx2 G A 17: 45,125,079 (GRCm39) P80L probably damaging Het
Scn5a T G 9: 119,314,996 (GRCm39) E1904A probably damaging Het
Sec16a G T 2: 26,326,014 (GRCm39) S240* probably null Het
Slc22a8 C T 19: 8,582,781 (GRCm39) T154I probably benign Het
Slc25a16 T A 10: 62,773,233 (GRCm39) V156E possibly damaging Het
Slc28a3 A T 13: 58,758,618 (GRCm39) S2T probably benign Het
Srd5a3 G A 5: 76,297,713 (GRCm39) V48I probably benign Het
Srebf1 A C 11: 60,091,352 (GRCm39) H1025Q probably damaging Het
Stard9 A G 2: 120,527,672 (GRCm39) K1310E probably benign Het
Swt1 A G 1: 151,246,381 (GRCm39) V848A possibly damaging Het
Tanc2 A T 11: 105,731,525 (GRCm39) T434S possibly damaging Het
Tcf20 G A 15: 82,738,883 (GRCm39) T856I probably benign Het
Tcf7l2 T C 19: 55,883,165 (GRCm39) probably null Het
Trim45 A G 3: 100,839,195 (GRCm39) probably benign Het
Tsen2 T A 6: 115,524,933 (GRCm39) M44K possibly damaging Het
Ttc21a T A 9: 119,787,139 (GRCm39) C715* probably null Het
Vmn2r102 G A 17: 19,914,456 (GRCm39) V674I probably damaging Het
Zfp87 A G 13: 67,665,173 (GRCm39) S430P probably 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
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'- ATCTCTGTGTGACCTGAGGC -3'
(R):5'- CAACAGAAAGATGGCGCTCTC -3'

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