Incidental Mutation 'R6161:Nphp3'
ID 489877
Institutional Source Beutler Lab
Gene Symbol Nphp3
Ensembl Gene ENSMUSG00000032558
Gene Name nephronophthisis 3 (adolescent)
Synonyms 3632410F03Rik, D330020E01Rik, pcy, nephrocystin 3
MMRRC Submission 044308-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6161 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 104002544-104043818 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 104031906 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Asparagine to Aspartic acid at position 772 (N772D)
Ref Sequence ENSEMBL: ENSMUSP00000035167 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035167] [ENSMUST00000193439] [ENSMUST00000194183] [ENSMUST00000194774]
AlphaFold Q7TNH6
Predicted Effect probably benign
Transcript: ENSMUST00000035167
AA Change: N772D

PolyPhen 2 Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: N772D

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: N652D
SMART Domains Protein: ENSMUSP00000116459
Gene: ENSMUSG00000032558
AA Change: N652D

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: 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
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: N652D
SMART Domains Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: N652D

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
Meta Mutation Damage Score 0.0886 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 97.9%
  • 20x: 93.9%
Validation Efficiency 100% (54/54)
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 A T 7: 120,540,711 (GRCm38) K1533M probably damaging Het
Aldh1l2 C T 10: 83,520,338 (GRCm38) V63I probably benign Het
Atr A G 9: 95,865,319 (GRCm38) H218R probably benign Het
Atxn7l1 T A 12: 33,358,663 (GRCm38) S275T possibly damaging Het
Cacna1c T C 6: 119,057,302 (GRCm38) K88R probably damaging Het
Ccl7 T C 11: 82,046,586 (GRCm38) Y49H probably damaging Het
Cd3eap G A 7: 19,357,633 (GRCm38) T183I possibly damaging Het
Cers5 A G 15: 99,738,663 (GRCm38) probably null Het
Chuk T C 19: 44,082,637 (GRCm38) E543G probably damaging Het
Dip2c T C 13: 9,647,007 (GRCm38) V1318A probably damaging Het
Ercc5 A G 1: 44,167,352 (GRCm38) H475R probably benign Het
Fat3 A G 9: 16,377,522 (GRCm38) L235P probably damaging Het
Fbn1 A T 2: 125,369,801 (GRCm38) C892* probably null Het
Fbxw8 T C 5: 118,092,675 (GRCm38) T354A possibly damaging Het
Fsip2 A C 2: 82,987,257 (GRCm38) T4445P possibly damaging Het
Gpld1 A T 13: 24,971,414 (GRCm38) Q344L probably benign Het
Hao1 A T 2: 134,505,625 (GRCm38) D253E probably benign Het
Hmcn2 A G 2: 31,356,254 (GRCm38) D745G probably benign Het
Kcnt1 A G 2: 25,903,385 (GRCm38) T658A probably benign Het
Klhl35 A G 7: 99,473,337 (GRCm38) probably benign Het
Lnx2 C T 5: 147,042,026 (GRCm38) probably null Het
Map3k5 T C 10: 20,000,575 (GRCm38) V160A probably damaging Het
Masp2 A T 4: 148,614,012 (GRCm38) I517F possibly damaging Het
Mc4r A T 18: 66,859,180 (GRCm38) Y287* probably null Het
Mthfr A G 4: 148,041,754 (GRCm38) D94G probably benign Het
Muc16 A G 9: 18,647,818 (GRCm38) I2393T unknown Het
Mybbp1a G T 11: 72,446,012 (GRCm38) V557L probably damaging Het
Mycbp2 A T 14: 103,298,747 (GRCm38) W256R probably damaging Het
Nacad G A 11: 6,600,902 (GRCm38) S763L probably benign Het
Nebl A G 2: 17,730,830 (GRCm38) V11A probably benign Het
Notch1 A T 2: 26,468,731 (GRCm38) C1363S probably damaging Het
Nqo2 G A 13: 33,979,651 (GRCm38) V98M probably damaging Het
Pak4 A G 7: 28,565,267 (GRCm38) I70T possibly damaging Het
Pbx2 A G 17: 34,593,600 (GRCm38) K2E probably damaging Het
Pikfyve A G 1: 65,216,043 (GRCm38) T352A probably benign Het
Pop1 T C 15: 34,526,310 (GRCm38) Y684H probably damaging Het
Rpa1 A G 11: 75,314,895 (GRCm38) V212A probably damaging Het
Rpap2 A G 5: 107,620,670 (GRCm38) E458G probably damaging Het
Sin3a T C 9: 57,095,424 (GRCm38) V200A possibly damaging Het
Sla T C 15: 66,782,598 (GRCm38) T280A probably null Het
Slc22a26 A T 19: 7,786,447 (GRCm38) I406K possibly damaging Het
Slc24a1 T C 9: 64,937,263 (GRCm38) N606S unknown Het
Slc39a10 G A 1: 46,827,407 (GRCm38) T443M probably damaging Het
Smg1 A T 7: 118,163,330 (GRCm38) probably benign Het
Sra1 G A 18: 36,670,283 (GRCm38) A9V probably damaging Het
Stard4 A G 18: 33,209,056 (GRCm38) V47A probably damaging Het
Stat4 A T 1: 52,074,677 (GRCm38) D182V possibly damaging Het
Syt1 A G 10: 108,631,807 (GRCm38) F210L probably damaging Het
Ube2q1 T A 3: 89,781,360 (GRCm38) probably null Het
Vmn1r159 C T 7: 22,843,187 (GRCm38) C140Y possibly damaging Het
Wnt8a T C 18: 34,545,546 (GRCm38) F138L possibly damaging Het
Zfp623 T A 15: 75,948,621 (GRCm38) D475E probably benign Het
Zfp646 C T 7: 127,878,725 (GRCm38) R25W probably damaging Het
Other mutations in Nphp3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01707:Nphp3 APN 9 104,018,158 (GRCm38) missense possibly damaging 0.75
IGL02329:Nphp3 APN 9 104,025,968 (GRCm38) missense probably benign 0.19
lithograph UTSW 9 104,041,990 (GRCm38) missense probably damaging 1.00
quartzite UTSW 9 104,036,177 (GRCm38) missense probably damaging 1.00
F5770:Nphp3 UTSW 9 104,035,894 (GRCm38) critical splice donor site probably null
FR4548:Nphp3 UTSW 9 104,025,939 (GRCm38) small deletion probably benign
FR4589:Nphp3 UTSW 9 104,025,939 (GRCm38) small deletion probably benign
R0112:Nphp3 UTSW 9 104,037,348 (GRCm38) missense possibly damaging 0.80
R0555:Nphp3 UTSW 9 104,023,434 (GRCm38) missense probably damaging 1.00
R0632:Nphp3 UTSW 9 104,018,274 (GRCm38) missense probably damaging 1.00
R0674:Nphp3 UTSW 9 104,036,282 (GRCm38) critical splice donor site probably null
R0743:Nphp3 UTSW 9 104,022,768 (GRCm38) small deletion probably benign
R0853:Nphp3 UTSW 9 104,031,933 (GRCm38) missense probably benign 0.03
R0920:Nphp3 UTSW 9 104,031,907 (GRCm38) missense probably benign 0.00
R1420:Nphp3 UTSW 9 104,035,893 (GRCm38) critical splice donor site probably null
R1464:Nphp3 UTSW 9 104,031,879 (GRCm38) splice site probably benign
R1476:Nphp3 UTSW 9 104,025,927 (GRCm38) missense possibly damaging 0.81
R1585:Nphp3 UTSW 9 104,009,214 (GRCm38) missense probably damaging 1.00
R1608:Nphp3 UTSW 9 104,035,840 (GRCm38) missense probably benign 0.30
R1688:Nphp3 UTSW 9 104,003,124 (GRCm38) missense probably damaging 1.00
R1691:Nphp3 UTSW 9 104,002,811 (GRCm38) missense probably benign
R1807:Nphp3 UTSW 9 104,020,741 (GRCm38) missense probably benign 0.01
R1857:Nphp3 UTSW 9 104,021,294 (GRCm38) missense possibly damaging 0.87
R1962:Nphp3 UTSW 9 104,021,338 (GRCm38) missense probably benign 0.00
R2127:Nphp3 UTSW 9 104,008,243 (GRCm38) missense probably damaging 0.98
R2138:Nphp3 UTSW 9 104,025,903 (GRCm38) missense possibly damaging 0.89
R2233:Nphp3 UTSW 9 104,037,376 (GRCm38) missense probably benign 0.02
R2234:Nphp3 UTSW 9 104,037,376 (GRCm38) missense probably benign 0.02
R3861:Nphp3 UTSW 9 104,039,326 (GRCm38) unclassified probably benign
R3928:Nphp3 UTSW 9 104,011,730 (GRCm38) missense probably damaging 0.99
R3961:Nphp3 UTSW 9 104,003,042 (GRCm38) nonsense probably null
R4182:Nphp3 UTSW 9 104,038,464 (GRCm38) missense probably benign 0.06
R4294:Nphp3 UTSW 9 104,022,717 (GRCm38) missense probably damaging 1.00
R4387:Nphp3 UTSW 9 104,030,020 (GRCm38) missense possibly damaging 0.94
R4625:Nphp3 UTSW 9 104,036,159 (GRCm38) missense possibly damaging 0.66
R4628:Nphp3 UTSW 9 104,003,058 (GRCm38) missense probably damaging 0.99
R4696:Nphp3 UTSW 9 104,022,732 (GRCm38) missense probably benign 0.01
R4865:Nphp3 UTSW 9 104,031,970 (GRCm38) missense probably benign
R4886:Nphp3 UTSW 9 104,002,994 (GRCm38) missense probably damaging 1.00
R4973:Nphp3 UTSW 9 104,031,999 (GRCm38) missense probably benign
R5445:Nphp3 UTSW 9 104,004,723 (GRCm38) missense probably damaging 1.00
R5451:Nphp3 UTSW 9 104,042,022 (GRCm38) missense probably benign
R5520:Nphp3 UTSW 9 104,024,673 (GRCm38) missense probably benign 0.30
R5641:Nphp3 UTSW 9 104,036,153 (GRCm38) missense probably damaging 1.00
R5847:Nphp3 UTSW 9 104,003,037 (GRCm38) missense probably damaging 1.00
R5928:Nphp3 UTSW 9 104,035,797 (GRCm38) missense probably benign 0.01
R5931:Nphp3 UTSW 9 104,020,746 (GRCm38) missense probably damaging 1.00
R6298:Nphp3 UTSW 9 104,015,441 (GRCm38) missense probably damaging 1.00
R6890:Nphp3 UTSW 9 104,041,954 (GRCm38) missense probably damaging 0.96
R7009:Nphp3 UTSW 9 104,016,116 (GRCm38) missense probably null 0.00
R7065:Nphp3 UTSW 9 104,041,990 (GRCm38) missense probably damaging 1.00
R7146:Nphp3 UTSW 9 104,004,837 (GRCm38) nonsense probably null
R7198:Nphp3 UTSW 9 104,004,775 (GRCm38) missense probably damaging 1.00
R7360:Nphp3 UTSW 9 104,016,078 (GRCm38) critical splice acceptor site probably null
R7369:Nphp3 UTSW 9 104,018,250 (GRCm38) missense probably damaging 0.99
R7554:Nphp3 UTSW 9 104,042,071 (GRCm38) missense probably damaging 0.98
R7591:Nphp3 UTSW 9 104,018,278 (GRCm38) critical splice donor site probably null
R7665:Nphp3 UTSW 9 104,005,393 (GRCm38) splice site probably null
R7672:Nphp3 UTSW 9 104,031,960 (GRCm38) missense probably benign
R7675:Nphp3 UTSW 9 104,016,088 (GRCm38) missense probably benign
R8039:Nphp3 UTSW 9 104,031,963 (GRCm38) missense probably benign
R8145:Nphp3 UTSW 9 104,035,851 (GRCm38) missense probably benign 0.16
R8211:Nphp3 UTSW 9 104,031,897 (GRCm38) missense possibly damaging 0.80
R8882:Nphp3 UTSW 9 104,005,594 (GRCm38) missense possibly damaging 0.77
R9020:Nphp3 UTSW 9 104,031,951 (GRCm38) missense probably benign 0.00
R9132:Nphp3 UTSW 9 104,020,781 (GRCm38) missense probably damaging 1.00
R9135:Nphp3 UTSW 9 104,032,015 (GRCm38) missense probably damaging 0.99
R9159:Nphp3 UTSW 9 104,020,781 (GRCm38) missense probably damaging 1.00
R9204:Nphp3 UTSW 9 104,042,106 (GRCm38) missense probably benign
R9226:Nphp3 UTSW 9 104,008,129 (GRCm38) missense probably benign 0.00
R9229:Nphp3 UTSW 9 104,036,177 (GRCm38) missense probably damaging 1.00
R9526:Nphp3 UTSW 9 104,036,138 (GRCm38) missense probably damaging 1.00
R9678:Nphp3 UTSW 9 104,023,487 (GRCm38) missense possibly damaging 0.90
R9731:Nphp3 UTSW 9 104,009,170 (GRCm38) missense probably damaging 1.00
V7583:Nphp3 UTSW 9 104,035,894 (GRCm38) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- GCTAGTGTGCACATGTATGAAAG -3'
(R):5'- TGTTGGACAGGTTTCACATGC -3'

Sequencing Primer
(F):5'- GCACATGTATGAAAGTATGGATGTC -3'
(R):5'- GGACAGGTTTCACATGCAATTTAAAG -3'
Posted On 2017-10-10