Incidental Mutation 'R7065:Nphp3'
ID 548526
Institutional Source Beutler Lab
Gene Symbol Nphp3
Ensembl Gene ENSMUSG00000032558
Gene Name nephronophthisis 3 (adolescent)
Synonyms pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3
MMRRC Submission 045161-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7065 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 103879743-103921010 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 103919189 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 1279 (Y1279C)
Ref Sequence ENSEMBL: ENSMUSP00000035167 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035166] [ENSMUST00000035167] [ENSMUST00000193439] [ENSMUST00000194183] [ENSMUST00000194774] [ENSMUST00000216593]
AlphaFold Q7TNH6
Predicted Effect probably benign
Transcript: ENSMUST00000035166
SMART Domains Protein: ENSMUSP00000035166
Gene: ENSMUSG00000032557

DomainStartEndE-ValueType
coiled coil region 1 30 N/A INTRINSIC
Pfam:ThiF 51 309 2.8e-48 PFAM
low complexity region 317 332 N/A INTRINSIC
low complexity region 343 353 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000035167
AA Change: Y1279C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: Y1279C

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: ENSMUST00000147249
SMART Domains Protein: ENSMUSP00000115381
Gene: ENSMUSG00000101152

DomainStartEndE-ValueType
Pfam:TPR_12 1 48 3e-14 PFAM
Pfam:TPR_12 12 75 2.1e-14 PFAM
Pfam:TPR_10 15 56 7.8e-13 PFAM
Pfam:TPR_1 16 49 4.4e-9 PFAM
Pfam:TPR_7 18 58 7e-8 PFAM
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 probably benign
Transcript: ENSMUST00000194183
SMART Domains Protein: ENSMUSP00000142049
Gene: ENSMUSG00000032558

DomainStartEndE-ValueType
Pfam:TPR_10 1 37 3.4e-5 PFAM
Pfam:TPR_12 1 71 1.8e-14 PFAM
Pfam:TPR_10 38 79 6.5e-8 PFAM
Pfam:TPR_1 39 72 6.8e-4 PFAM
Pfam:TPR_10 81 115 9e-3 PFAM
Pfam:TPR_7 83 118 1.6e-2 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000194774
AA Change: Y1159C
SMART Domains Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: Y1159C

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
Predicted Effect probably benign
Transcript: ENSMUST00000216593
Meta Mutation Damage Score 0.2474 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 100% (62/62)
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca1 G T 4: 53,074,233 (GRCm39) S1150Y probably damaging Het
Abca13 T A 11: 9,242,595 (GRCm39) V1486E probably benign Het
Abca17 T A 17: 24,546,725 (GRCm39) Y292F probably damaging Het
Adam3 A G 8: 25,201,691 (GRCm39) probably null Het
Ankmy2 G A 12: 36,237,707 (GRCm39) E269K probably damaging Het
Cdan1 A G 2: 120,549,402 (GRCm39) S1201P probably benign Het
Cep57 T C 9: 13,729,677 (GRCm39) Y122C probably damaging Het
Cfh T A 1: 140,014,140 (GRCm39) Y1210F probably damaging Het
Cflar T G 1: 58,770,368 (GRCm39) L154V probably damaging Het
Chmp4b A G 2: 154,533,162 (GRCm39) D134G probably damaging Het
Clec14a A G 12: 58,315,580 (GRCm39) F14S possibly damaging Het
Ctnna1 A T 18: 35,285,669 (GRCm39) H5L probably benign Het
Cyp2e1 T A 7: 140,343,906 (GRCm39) L48Q probably damaging Het
Dnah6 T G 6: 73,064,545 (GRCm39) Q2627P possibly damaging Het
Ehmt1 T C 2: 24,730,709 (GRCm39) D569G probably damaging Het
Frmd4a G A 2: 4,570,923 (GRCm39) Het
Fryl T C 5: 73,248,099 (GRCm39) D1006G probably damaging Het
Gclm A G 3: 122,056,320 (GRCm39) N137D probably benign Het
Gk5 A G 9: 96,061,109 (GRCm39) Y531C probably damaging Het
Gpm6a C A 8: 55,490,493 (GRCm39) N56K probably benign Het
Grik4 A C 9: 42,455,127 (GRCm39) V656G probably damaging Het
Grip2 C A 6: 91,760,550 (GRCm39) probably null Het
Gucy2c T C 6: 136,697,764 (GRCm39) K636E probably damaging Het
Ifi44l A G 3: 151,465,429 (GRCm39) I107T Het
Kif1b T C 4: 149,286,982 (GRCm39) T1237A possibly damaging Het
Klk1b11 A G 7: 43,648,386 (GRCm39) D131G probably benign Het
Lipe A G 7: 25,084,603 (GRCm39) probably null Het
Lrp4 A G 2: 91,341,925 (GRCm39) D1846G probably damaging Het
Madd A T 2: 90,985,402 (GRCm39) M1273K probably benign Het
Matn3 T A 12: 9,002,472 (GRCm39) M228K probably damaging Het
Mterf4 T A 1: 93,232,617 (GRCm39) H78L probably benign Het
Ncoa4 T A 14: 31,894,857 (GRCm39) L128* probably null Het
Nedd4l A G 18: 65,329,040 (GRCm39) N627S probably benign Het
Niban1 A G 1: 151,575,858 (GRCm39) probably null Het
Nrp1 C A 8: 129,187,193 (GRCm39) T413N probably benign Het
Opn4 C A 14: 34,317,834 (GRCm39) A267S probably benign Het
Or4c11c A T 2: 88,661,730 (GRCm39) I90F probably damaging Het
Or5ak24 A G 2: 85,260,523 (GRCm39) Y217H probably damaging Het
Or5al6 A C 2: 85,976,345 (GRCm39) H244Q probably damaging Het
Or5p78 G A 7: 108,212,266 (GRCm39) V251I probably damaging Het
Pax3 T C 1: 78,170,648 (GRCm39) probably null Het
Pcdha12 A G 18: 37,154,679 (GRCm39) E466G probably damaging Het
Pdzk1 A G 3: 96,775,748 (GRCm39) E372G probably benign Het
Pigs T A 11: 78,227,565 (GRCm39) V243D possibly damaging Het
Pla2g5 C A 4: 138,527,915 (GRCm39) C117F probably damaging Het
Ppt2 A G 17: 34,841,829 (GRCm39) S236P probably damaging Het
Raver1 T C 9: 21,001,590 (GRCm39) D81G probably benign Het
Rpgrip1 T C 14: 52,378,650 (GRCm39) L525P possibly damaging Het
Ryr1 T C 7: 28,803,068 (GRCm39) E662G probably damaging Het
Scaf8 G A 17: 3,209,486 (GRCm39) V66M probably damaging Het
Scn3a A C 2: 65,295,199 (GRCm39) L1508R probably benign Het
Semp2l2b T C 10: 21,943,197 (GRCm39) D261G probably benign Het
Slfn8 T C 11: 82,907,794 (GRCm39) R250G probably benign Het
Speer4d A C 5: 15,825,421 (GRCm39) T49P probably damaging Het
Spice1 T A 16: 44,175,898 (GRCm39) D32E probably damaging Het
Stt3b A G 9: 115,095,224 (GRCm39) L269P probably damaging Het
Ttn A G 2: 76,628,456 (GRCm39) I14568T possibly damaging Het
U2surp T C 9: 95,367,712 (GRCm39) T413A probably benign Het
Ubr3 A G 2: 69,784,049 (GRCm39) E755G probably damaging Het
Unc5a A T 13: 55,138,896 (GRCm39) S92C probably damaging Het
Zfat T C 15: 68,052,969 (GRCm39) Y275C probably damaging Het
Zfp874a A T 13: 67,590,401 (GRCm39) S428T probably damaging Het
Zfy1 A G Y: 725,428 (GRCm39) V779A probably benign 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
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'- GCAGGTGATAACAACACTTAGC -3'
(R):5'- TGCCAGCTAAATAACACTAAGATGG -3'

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