Incidental Mutation 'R4628:Nphp3'
ID 348967
Institutional Source Beutler Lab
Gene Symbol Nphp3
Ensembl Gene ENSMUSG00000032558
Gene Name nephronophthisis 3 (adolescent)
Synonyms pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3
MMRRC Submission 041893-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4628 (G1)
Quality Score 189
Status Not validated
Chromosome 9
Chromosomal Location 103879743-103921010 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 103880257 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 93 (E93G)
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: E93G

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: E93G

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 noncoding transcript
Transcript: ENSMUST00000191919
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 probably benign
Transcript: ENSMUST00000194774
SMART Domains Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558

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 noncoding transcript
Transcript: ENSMUST00000216588
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.3%
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: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca7 G T 10: 79,851,022 (GRCm39) probably null Het
Abcb4 A G 5: 8,957,399 (GRCm39) D176G probably benign Het
Adamts18 C T 8: 114,499,800 (GRCm39) W371* probably null Het
Akr1c13 G T 13: 4,247,869 (GRCm39) V214F probably damaging Het
Alkbh2 C T 5: 114,262,287 (GRCm39) E148K probably damaging Het
Ankrd12 T C 17: 66,292,989 (GRCm39) T815A probably benign Het
Arid3a T C 10: 79,766,992 (GRCm39) S89P possibly damaging Het
Ass1 A T 2: 31,371,000 (GRCm39) D63V probably damaging Het
Atxn3 T A 12: 101,889,337 (GRCm39) probably benign Het
Bcap29 C T 12: 31,676,806 (GRCm39) S88N probably benign Het
Bsn G T 9: 107,990,434 (GRCm39) P1773T probably damaging Het
Ccdc141 A G 2: 76,890,024 (GRCm39) S423P probably benign Het
Cfap46 A T 7: 139,260,843 (GRCm39) L85Q probably damaging Het
Chd8 T C 14: 52,444,372 (GRCm39) R438G probably benign Het
Chd9 T A 8: 91,710,091 (GRCm39) M289K probably benign Het
Col14a1 T A 15: 55,313,229 (GRCm39) Y26* probably null Het
Colec10 A G 15: 54,323,127 (GRCm39) T117A possibly damaging Het
Colq C A 14: 31,265,979 (GRCm39) G178V probably damaging Het
Defb3 A T 8: 19,345,156 (GRCm39) R37S probably benign Het
Duox1 A G 2: 122,176,733 (GRCm39) Y1418C probably damaging Het
Engase C T 11: 118,375,731 (GRCm39) S33F probably damaging Het
Erich3 A T 3: 154,469,324 (GRCm39) T1259S probably damaging Het
Fam98c T C 7: 28,854,693 (GRCm39) T49A possibly damaging Het
Fhod3 T A 18: 25,253,186 (GRCm39) F1379I possibly damaging Het
Fndc3b T C 3: 27,610,277 (GRCm39) I86V probably benign Het
Gm1123 A G 9: 98,896,289 (GRCm39) V197A probably damaging Het
Gm4847 A T 1: 166,457,964 (GRCm39) V463E probably damaging Het
Gm9772 T C 17: 22,226,188 (GRCm39) K32R probably damaging Het
Gm9804 T C 12: 49,448,540 (GRCm39) S161P unknown Het
Gpr162 C T 6: 124,838,405 (GRCm39) D82N probably benign Het
Grid2ip T C 5: 143,368,630 (GRCm39) V650A probably damaging Het
Hs1bp3 T C 12: 8,386,357 (GRCm39) V253A probably benign Het
Hsd3b6 T G 3: 98,713,895 (GRCm39) K135Q possibly damaging Het
Igfn1 T C 1: 135,887,468 (GRCm39) D2532G possibly damaging Het
Iqgap2 A G 13: 95,899,837 (GRCm39) Y74H probably benign Het
Itga2 A G 13: 115,014,229 (GRCm39) V233A probably benign Het
Kat14 A G 2: 144,246,140 (GRCm39) probably benign Het
Kctd21 A G 7: 96,996,782 (GRCm39) D85G probably damaging Het
Kera A G 10: 97,445,493 (GRCm39) N284S probably benign Het
Krt1 C T 15: 101,754,622 (GRCm39) G543S unknown Het
Lcmt1 T A 7: 123,010,035 (GRCm39) C183* probably null Het
Lcn5 A G 2: 25,548,075 (GRCm39) E28G possibly damaging Het
Leo1 A T 9: 75,352,979 (GRCm39) D174V probably damaging Het
Llgl1 A T 11: 60,600,811 (GRCm39) T636S probably damaging Het
Lrrc8e T A 8: 4,283,981 (GRCm39) C69S probably damaging Het
Maml3 A T 3: 51,703,891 (GRCm39) probably benign Het
Maz G T 7: 126,624,519 (GRCm39) H334N possibly damaging Het
Mcm6 T C 1: 128,279,285 (GRCm39) D167G probably benign Het
Mrpl24 A C 3: 87,829,436 (GRCm39) probably null Het
Myo18a G A 11: 77,714,962 (GRCm39) V834M probably damaging Het
Neb T A 2: 52,198,362 (GRCm39) R461* probably null Het
Notch4 C A 17: 34,789,159 (GRCm39) T486N probably damaging Het
Nup188 A G 2: 30,219,358 (GRCm39) Y858C probably damaging Het
Or13a17 T A 7: 140,271,291 (GRCm39) S158T probably benign Het
Or13a28 C T 7: 140,218,297 (GRCm39) R228C probably benign Het
Or1j11 T A 2: 36,311,869 (GRCm39) L153* probably null Het
Otud4 T A 8: 80,366,597 (GRCm39) D21E possibly damaging Het
Ovgp1 T A 3: 105,887,639 (GRCm39) probably null Het
Pdia3 A T 2: 121,244,620 (GRCm39) N11I possibly damaging Het
Pex5 T C 6: 124,380,079 (GRCm39) D286G possibly damaging Het
Pias3 T C 3: 96,607,136 (GRCm39) I133T probably damaging Het
Postn A G 3: 54,279,578 (GRCm39) D352G probably damaging Het
Prl7c1 T C 13: 27,962,065 (GRCm39) R81G probably benign Het
Rmi1 A G 13: 58,556,950 (GRCm39) R400G probably benign Het
Rtraf T A 14: 19,867,155 (GRCm39) N116I probably benign Het
Semp2l2a T A 8: 13,886,625 (GRCm39) R489W probably damaging Het
Slc6a12 T A 6: 121,328,951 (GRCm39) C50* probably null Het
Spring1 G C 5: 118,397,479 (GRCm39) A154P probably damaging Het
Srcin1 T A 11: 97,439,752 (GRCm39) H126L probably benign Het
Tmtc2 A T 10: 105,139,511 (GRCm39) S672T probably benign Het
Top2b T G 14: 16,409,189 (GRCm38) I777M probably damaging Het
Ube2c A G 2: 164,614,093 (GRCm39) N143S possibly damaging Het
Uroc1 A T 6: 90,332,310 (GRCm39) I556F probably damaging Het
Vmn1r124 T A 7: 20,994,302 (GRCm39) K81* probably null Het
Vmn1r57 T A 7: 5,223,972 (GRCm39) C166S probably damaging Het
Vmn2r114 ATTT ATT 17: 23,509,906 (GRCm39) probably null Het
Vmn2r68 A G 7: 84,883,673 (GRCm39) V144A probably benign Het
Vmn2r85 C T 10: 130,261,235 (GRCm39) M367I probably benign Het
Vwa3a T A 7: 120,392,598 (GRCm39) N812K probably benign Het
Wdfy4 A T 14: 32,824,515 (GRCm39) N1301K probably damaging Het
Zfhx4 G A 3: 5,468,536 (GRCm39) R2898H 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
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'- TGGAAGTGAAACCCAAGGCC -3'
(R):5'- AAACAACTTGGTTTGTAGCTGG -3'

Sequencing Primer
(F):5'- TGGGCGCCAGCTTCAAG -3'
(R):5'- ACAACTTGGTTTGTAGCTGGGGTAG -3'
Posted On 2015-10-08