Incidental Mutation 'R2138:Nphp3'
ID 235967
Institutional Source Beutler Lab
Gene Symbol Nphp3
Ensembl Gene ENSMUSG00000032558
Gene Name nephronophthisis 3 (adolescent)
Synonyms pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3
MMRRC Submission 040141-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2138 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 103879743-103921010 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 103903102 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 693 (E693G)
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: E693G

PolyPhen 2 Score 0.892 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: E693G

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: E573G
SMART Domains Protein: ENSMUSP00000116459
Gene: ENSMUSG00000032558
AA Change: E573G

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: E573G
SMART Domains Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: E573G

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: 99.2%
  • 3x: 98.7%
  • 10x: 97.4%
  • 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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aamp A G 1: 74,323,122 (GRCm39) V6A probably benign Het
Abcc6 A G 7: 45,630,475 (GRCm39) F1262L probably damaging Het
Acot13 A T 13: 25,002,188 (GRCm39) probably null Het
Adgrv1 T C 13: 81,593,439 (GRCm39) I4183V probably benign Het
Aff4 T G 11: 53,263,339 (GRCm39) S120A possibly damaging Het
Afp A G 5: 90,647,506 (GRCm39) E250G probably damaging Het
Ankrd34b A T 13: 92,575,914 (GRCm39) D382V probably damaging Het
Arhgef19 A T 4: 140,978,111 (GRCm39) I577F probably damaging Het
Arl6 A G 16: 59,442,830 (GRCm39) probably benign Het
Atp2b2 A T 6: 113,773,268 (GRCm39) M333K probably benign Het
Atp8b3 C A 10: 80,362,939 (GRCm39) A635S possibly damaging Het
Baiap2 A G 11: 119,847,928 (GRCm39) T19A possibly damaging Het
Bcar3 A G 3: 122,306,645 (GRCm39) D206G probably damaging Het
Ccdc162 A T 10: 41,457,293 (GRCm39) M85K probably benign Het
Clec4a4 A G 6: 123,000,937 (GRCm39) N217D probably damaging Het
Csmd1 T C 8: 15,979,088 (GRCm39) Y2832C probably damaging Het
Cubn A G 2: 13,449,189 (GRCm39) I962T probably damaging Het
Dennd4a A G 9: 64,796,619 (GRCm39) Y852C probably damaging Het
Dhcr24 G T 4: 106,429,499 (GRCm39) E191* probably null Het
Dusp12 G A 1: 170,708,166 (GRCm39) Q114* probably null Het
Elfn2 G T 15: 78,558,238 (GRCm39) T103K probably benign Het
Eme1 A T 11: 94,539,018 (GRCm39) V314E probably damaging Het
Epb41l3 A G 17: 69,514,875 (GRCm39) E4G probably damaging Het
Exoc6b A T 6: 84,966,464 (GRCm39) L170Q probably damaging Het
Fbln5 C T 12: 101,728,179 (GRCm39) M261I probably benign Het
Fgf22 T C 10: 79,592,435 (GRCm39) V64A probably damaging Het
Gak C T 5: 108,754,743 (GRCm39) probably null Het
Gatad2b T A 3: 90,259,420 (GRCm39) S401R probably damaging Het
Gen1 A T 12: 11,291,622 (GRCm39) S722R probably damaging Het
Gm10754 A T 10: 97,518,132 (GRCm39) probably benign Het
Grid2 G A 6: 64,322,782 (GRCm39) R594Q probably damaging Het
Grm7 C A 6: 110,623,098 (GRCm39) N90K probably damaging Het
Herc1 G A 9: 66,377,589 (GRCm39) V3452M possibly damaging Het
Il22ra2 T A 10: 19,508,618 (GRCm39) F215L probably benign Het
Kank1 G A 19: 25,389,117 (GRCm39) G930D probably benign Het
Klra3 A T 6: 130,310,121 (GRCm39) V133D probably benign Het
Lims2 A G 18: 32,088,460 (GRCm39) E220G possibly damaging Het
Mbd3l2 A T 9: 18,356,254 (GRCm39) D193V probably damaging Het
Mbl1 T A 14: 40,875,648 (GRCm39) I34K possibly damaging Het
Mgam C T 6: 40,733,384 (GRCm39) P839S probably damaging Het
Mmp9 G T 2: 164,794,387 (GRCm39) E460* probably null Het
Mov10 T C 3: 104,711,558 (GRCm39) H316R probably benign Het
Ms4a18 A T 19: 10,974,695 (GRCm39) V332D possibly damaging Het
Myo15b T C 11: 115,774,633 (GRCm39) S2082P probably benign Het
Myrfl G A 10: 116,631,443 (GRCm39) T706I probably benign Het
Nampt C A 12: 32,888,421 (GRCm39) H191N possibly damaging Het
Niban1 G A 1: 151,572,002 (GRCm39) V316M probably damaging Het
Obscn A T 11: 58,894,491 (GRCm39) Y1191* probably null Het
Or10z1 A T 1: 174,078,302 (GRCm39) probably null Het
Or1r1 A T 11: 73,875,129 (GRCm39) Y102N probably damaging Het
Or7a40 A G 16: 16,491,069 (GRCm39) Y259H probably damaging Het
Osbpl10 A G 9: 115,061,202 (GRCm39) N760S probably benign Het
Otof A G 5: 30,619,114 (GRCm39) V10A probably benign Het
Pkhd1l1 A C 15: 44,364,853 (GRCm39) E664A probably damaging Het
Pnp2 T C 14: 51,201,161 (GRCm39) S178P probably damaging Het
Pvr G A 7: 19,650,927 (GRCm39) T199I probably damaging Het
Rbp3 C T 14: 33,677,975 (GRCm39) T641M probably damaging Het
Rnaseh2b T C 14: 62,598,794 (GRCm39) V173A probably benign Het
Septin12 C T 16: 4,810,070 (GRCm39) R155H probably damaging Het
Slco6d1 G T 1: 98,371,385 (GRCm39) R290L probably benign Het
Snx32 A G 19: 5,546,157 (GRCm39) V335A probably damaging Het
Son T C 16: 91,456,260 (GRCm39) V1669A possibly damaging Het
Speer1f A T 5: 11,469,052 (GRCm39) R68* probably null Het
Tbata C T 10: 61,015,063 (GRCm39) T116I probably benign Het
Tdrd1 T A 19: 56,831,021 (GRCm39) S279T probably benign Het
Thsd7a A T 6: 12,471,072 (GRCm39) Y515* probably null Het
Tmem102 T G 11: 69,695,940 (GRCm39) L40F probably damaging Het
Tmem169 A G 1: 72,340,155 (GRCm39) N195S probably damaging Het
Tmem201 A T 4: 149,802,537 (GRCm39) S613T probably damaging Het
Tnfaip6 A T 2: 51,942,344 (GRCm39) I218F possibly damaging Het
Tube1 C A 10: 39,023,347 (GRCm39) H331Q probably benign Het
Wwc1 G A 11: 35,732,714 (GRCm39) T998I possibly damaging Het
Xpc A T 6: 91,475,104 (GRCm39) Y638* probably null Het
Zdhhc4 A T 5: 143,310,017 (GRCm39) Y80* 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
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
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'- CCCTTCTGCAACTGGAAGTC -3'
(R):5'- CCTGTTAAACTGGAATGAGCAGC -3'

Sequencing Primer
(F):5'- CAACTGGAAGTCTGGCCATAGC -3'
(R):5'- TCTGCTGAGAGACTGGACTGC -3'
Posted On 2014-10-01