Incidental Mutation 'R4625:Nphp3'
ID 346499
Institutional Source Beutler Lab
Gene Symbol Nphp3
Ensembl Gene ENSMUSG00000032558
Gene Name nephronophthisis 3 (adolescent)
Synonyms pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3
MMRRC Submission 041890-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4625 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 103879743-103921010 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 103913358 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Arginine at position 997 (G997R)
Ref Sequence ENSEMBL: ENSMUSP00000035167 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035167] [ENSMUST00000193439] [ENSMUST00000194183] [ENSMUST00000194774] [ENSMUST00000216593]
AlphaFold Q7TNH6
Predicted Effect possibly damaging
Transcript: ENSMUST00000035167
AA Change: G997R

PolyPhen 2 Score 0.664 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: G997R

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: G877R
SMART Domains Protein: ENSMUSP00000116459
Gene: ENSMUSG00000032558
AA Change: G877R

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: 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 noncoding transcript
Transcript: ENSMUST00000192485
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: ENSMUST00000194183
AA Change: G56R

PolyPhen 2 Score 0.450 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000142049
Gene: ENSMUSG00000032558
AA Change: G56R

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: G877R
SMART Domains Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: G877R

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 0.1795 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.1%
Validation Efficiency 97% (75/77)
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700018F24Rik A C 5: 144,981,693 (GRCm39) E176A possibly damaging Het
Abcc2 A G 19: 43,792,178 (GRCm39) I320V probably benign Het
Abtb1 C T 6: 88,813,269 (GRCm39) A466T probably benign Het
Ak6 C A 13: 100,792,181 (GRCm39) T208K probably benign Het
Albfm1 G T 5: 90,719,611 (GRCm39) V236L probably damaging Het
Alkbh2 C T 5: 114,262,287 (GRCm39) E148K probably damaging Het
Anapc15 T A 7: 101,550,239 (GRCm39) probably benign Het
Anxa2r1 G T 13: 120,496,765 (GRCm39) R35S possibly damaging Het
Aopep T C 13: 63,215,906 (GRCm39) S393P probably benign Het
Aspn A G 13: 49,710,901 (GRCm39) D182G probably benign Het
Astn1 A T 1: 158,407,864 (GRCm39) D607V probably damaging Het
Btnl1 A G 17: 34,598,725 (GRCm39) I114V probably null Het
Ccdc159 A G 9: 21,840,762 (GRCm39) S110G probably benign Het
Cdh18 A C 15: 22,714,128 (GRCm39) probably benign Het
Cdh22 A G 2: 164,954,526 (GRCm39) I665T probably damaging Het
Cenpk T A 13: 104,385,901 (GRCm39) H265Q possibly damaging Het
Chd6 A G 2: 160,811,412 (GRCm39) L1397P probably damaging Het
Chia1 A C 3: 106,036,256 (GRCm39) N279H probably benign Het
Cyp8b1 T C 9: 121,744,651 (GRCm39) E227G probably damaging Het
Dmxl2 A T 9: 54,311,404 (GRCm39) N1772K possibly damaging Het
Dnah2 A G 11: 69,354,487 (GRCm39) S2244P probably damaging Het
Fshr T C 17: 89,293,148 (GRCm39) Y510C probably damaging Het
Gm5087 T C 14: 13,158,798 (GRCm38) noncoding transcript Het
Gm7135 A C 1: 97,387,351 (GRCm39) noncoding transcript Het
Hnrnpll A T 17: 80,358,291 (GRCm39) Y153* probably null Het
Htt T A 5: 34,987,129 (GRCm39) V1116E probably damaging Het
Ikzf5 A T 7: 130,995,482 (GRCm39) probably null Het
Kcnb1 A G 2: 167,030,153 (GRCm39) S131P probably damaging Het
Kcnd3 C T 3: 105,566,082 (GRCm39) A421V probably damaging 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
Kif1a A T 1: 92,970,381 (GRCm39) D952E probably benign Het
Klf4 A G 4: 55,530,370 (GRCm39) V247A probably benign Het
Krt1 C T 15: 101,754,622 (GRCm39) G543S unknown Het
Lamc1 A G 1: 153,118,442 (GRCm39) S910P probably benign Het
Lin9 T A 1: 180,516,845 (GRCm39) N512K probably damaging Het
Mroh2a A T 1: 88,182,687 (GRCm39) N1205I possibly damaging Het
Mrps30 A G 13: 118,523,250 (GRCm39) V174A probably benign Het
Myo1g T C 11: 6,462,240 (GRCm39) E574G probably damaging Het
Obscn A G 11: 58,958,084 (GRCm39) C3748R probably damaging Het
Or1j17 A G 2: 36,578,083 (GRCm39) D23G probably benign Het
Or5p69 T C 7: 107,966,895 (GRCm39) L66P probably damaging Het
Or8g28 A T 9: 39,169,614 (GRCm39) M118K probably damaging Het
Or9s18 T A 13: 65,300,674 (GRCm39) V212D possibly damaging Het
Orc5 G T 5: 22,753,003 (GRCm39) F10L probably benign Het
Ptch1 T C 13: 63,670,978 (GRCm39) T851A probably benign Het
Ranbp6 A T 19: 29,788,263 (GRCm39) Y696* probably null Het
Rbp3 A G 14: 33,678,056 (GRCm39) Q668R probably benign Het
Rfwd3 T C 8: 112,002,990 (GRCm39) T611A probably benign Het
Rhcg T A 7: 79,251,352 (GRCm39) D219V probably damaging Het
Rmi1 A G 13: 58,556,950 (GRCm39) R400G probably benign Het
Slc25a26 G T 6: 94,484,633 (GRCm39) V58F probably damaging Het
Smarca5 T A 8: 81,437,192 (GRCm39) K721N probably damaging Het
Sp110 A C 1: 85,505,050 (GRCm39) F434C probably benign Het
Speer2 A T 16: 69,655,642 (GRCm39) Y61* probably null Het
Spef2 T C 15: 9,647,524 (GRCm39) Y961C probably damaging Het
Sptb C A 12: 76,634,100 (GRCm39) probably null Het
Svep1 T G 4: 58,072,698 (GRCm39) N2204H probably damaging Het
Tex56 G A 13: 35,116,448 (GRCm39) G66S probably damaging Het
Tmem86a C A 7: 46,702,613 (GRCm39) P13T probably damaging Het
Tmt1a A T 15: 100,210,939 (GRCm39) Q170L probably damaging Het
Tmtc2 A T 10: 105,139,511 (GRCm39) S672T probably benign Het
Tox2 G A 2: 163,156,336 (GRCm39) S211N possibly damaging Het
Trpc6 A T 9: 8,677,963 (GRCm39) E762D probably benign Het
Tshb C T 3: 102,685,461 (GRCm39) probably null Het
Ttc3 T A 16: 94,189,131 (GRCm39) L163* probably null Het
Twsg1 G T 17: 66,236,546 (GRCm39) D161E probably benign Het
Uchl4 A C 9: 64,143,080 (GRCm39) D187A probably damaging Het
Vmn2r104 A T 17: 20,268,443 (GRCm39) W9R probably benign Het
Yju2 T A 17: 56,271,598 (GRCm39) L173Q probably damaging Het
Zfp14 G A 7: 29,738,020 (GRCm39) Q322* probably null Het
Znhit3 G A 11: 84,802,316 (GRCm39) P145S 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
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'- GGATGACTCACGTTTACACCTC -3'
(R):5'- AAACACCCATTCGCTTCGTG -3'

Sequencing Primer
(F):5'- TCTCTCCTCCCAGGACGG -3'
(R):5'- CCATTCGCTTCGTGAGGTCTG -3'
Posted On 2015-09-25