Incidental Mutation 'R4696:Nphp3'
| ID |
355706 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nphp3
|
| Ensembl Gene |
ENSMUSG00000032558 |
| Gene Name |
nephronophthisis 3 (adolescent) |
| Synonyms |
pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3 |
| MMRRC Submission |
041946-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4696 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
103879743-103921010 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 103899931 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Arginine
at position 481
(H481R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141596
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000035167]
[ENSMUST00000193439]
[ENSMUST00000194774]
|
| AlphaFold |
Q7TNH6 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000035167
AA Change: H601R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: H601R
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
|
| SMART Domains |
Protein: ENSMUSP00000116459
Gene: ENSMUSG00000032558
AA Change: H481R
| Domain | Start | End | E-Value | Type |
|---|
|
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
AA Change: H507R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000141540
Gene: ENSMUSG00000032558
AA Change: H507R
| Domain | Start | End | E-Value | Type |
|---|
|
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
AA Change: H481R
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: H481R
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.9%
|
| Validation Efficiency |
99% (74/75) |
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc3 |
T |
C |
11: 94,241,817 (GRCm39) |
S1405G |
probably benign |
Het |
| Acaca |
T |
C |
11: 84,171,261 (GRCm39) |
V1165A |
possibly damaging |
Het |
| Acin1 |
C |
A |
14: 54,880,474 (GRCm39) |
|
probably benign |
Het |
| Akr1b8 |
G |
A |
6: 34,340,312 (GRCm39) |
V159I |
probably benign |
Het |
| Alms1 |
T |
C |
6: 85,597,504 (GRCm39) |
Y777H |
probably damaging |
Het |
| Cblc |
C |
A |
7: 19,530,407 (GRCm39) |
G101C |
probably damaging |
Het |
| Cdc42ep5 |
G |
A |
7: 4,154,614 (GRCm39) |
P58L |
possibly damaging |
Het |
| Cic |
A |
G |
7: 24,987,908 (GRCm39) |
N1532S |
probably benign |
Het |
| Cipc |
T |
A |
12: 86,999,714 (GRCm39) |
|
probably benign |
Het |
| Clca4b |
T |
C |
3: 144,617,146 (GRCm39) |
I835V |
probably benign |
Het |
| Cntrob |
C |
T |
11: 69,211,714 (GRCm39) |
G170D |
probably damaging |
Het |
| Col14a1 |
A |
G |
15: 55,235,998 (GRCm39) |
Q304R |
unknown |
Het |
| Csmd3 |
T |
C |
15: 47,777,364 (GRCm39) |
T1181A |
probably benign |
Het |
| Dchs1 |
A |
G |
7: 105,413,834 (GRCm39) |
F994L |
probably damaging |
Het |
| Ddx42 |
C |
A |
11: 106,138,529 (GRCm39) |
A776D |
probably benign |
Het |
| Disp2 |
G |
T |
2: 118,622,165 (GRCm39) |
E966* |
probably null |
Het |
| Dmpk |
A |
T |
7: 18,822,139 (GRCm39) |
N366Y |
probably damaging |
Het |
| Dmrt1 |
A |
G |
19: 25,580,674 (GRCm39) |
Y362C |
possibly damaging |
Het |
| Dock10 |
C |
T |
1: 80,493,330 (GRCm39) |
G1880D |
possibly damaging |
Het |
| Dzip1l |
A |
G |
9: 99,545,664 (GRCm39) |
R638G |
possibly damaging |
Het |
| Dzip3 |
T |
A |
16: 48,746,332 (GRCm39) |
|
probably benign |
Het |
| Ear-ps2 |
G |
A |
14: 44,284,517 (GRCm39) |
|
noncoding transcript |
Het |
| Eno4 |
T |
C |
19: 58,934,068 (GRCm39) |
S90P |
probably damaging |
Het |
| Epn2 |
C |
G |
11: 61,426,129 (GRCm39) |
A283P |
probably damaging |
Het |
| Eya3 |
T |
A |
4: 132,397,543 (GRCm39) |
Y67* |
probably null |
Het |
| Fat2 |
T |
C |
11: 55,175,841 (GRCm39) |
N1624S |
probably benign |
Het |
| Fez1 |
T |
A |
9: 36,781,766 (GRCm39) |
|
probably null |
Het |
| Fgfr1 |
T |
C |
8: 26,053,504 (GRCm39) |
S260P |
probably damaging |
Het |
| Glb1 |
A |
G |
9: 114,293,220 (GRCm39) |
S532G |
probably benign |
Het |
| Gm15455 |
A |
T |
1: 33,876,874 (GRCm39) |
|
noncoding transcript |
Het |
| Grid2ip |
A |
G |
5: 143,377,131 (GRCm39) |
|
probably benign |
Het |
| Guca2b |
C |
A |
4: 119,513,996 (GRCm39) |
G129V |
probably damaging |
Het |
| Hes3 |
T |
C |
4: 152,372,124 (GRCm39) |
E65G |
probably damaging |
Het |
| Itgbl1 |
T |
C |
14: 124,204,120 (GRCm39) |
C404R |
probably damaging |
Het |
| Kansl1 |
C |
T |
11: 104,247,593 (GRCm39) |
V586I |
possibly damaging |
Het |
| Krt18 |
A |
G |
15: 101,940,293 (GRCm39) |
D390G |
probably benign |
Het |
| Laptm5 |
T |
C |
4: 130,660,982 (GRCm39) |
|
probably benign |
Het |
| Lgals3bp |
C |
T |
11: 118,288,977 (GRCm39) |
E116K |
probably benign |
Het |
| Lrrc39 |
C |
T |
3: 116,363,769 (GRCm39) |
S114F |
probably damaging |
Het |
| Mfap3 |
T |
C |
11: 57,419,117 (GRCm39) |
|
probably null |
Het |
| Ntm |
T |
C |
9: 29,090,501 (GRCm39) |
T73A |
possibly damaging |
Het |
| Or5m13b |
T |
A |
2: 85,749,215 (GRCm39) |
|
probably null |
Het |
| Or8g4 |
T |
A |
9: 39,662,024 (GRCm39) |
M114K |
probably damaging |
Het |
| Pbk |
G |
A |
14: 66,049,386 (GRCm39) |
C21Y |
probably benign |
Het |
| Pglyrp1 |
A |
G |
7: 18,618,871 (GRCm39) |
E74G |
probably benign |
Het |
| R3hdm1 |
G |
T |
1: 128,164,503 (GRCm39) |
|
probably benign |
Het |
| Rap1gds1 |
T |
C |
3: 138,633,375 (GRCm39) |
T599A |
probably damaging |
Het |
| Rigi |
A |
G |
4: 40,203,798 (GRCm39) |
|
probably benign |
Het |
| Rims1 |
A |
T |
1: 22,358,836 (GRCm39) |
M1273K |
probably damaging |
Het |
| Sbf1 |
G |
A |
15: 89,187,315 (GRCm39) |
R721* |
probably null |
Het |
| Slc17a1 |
T |
C |
13: 24,064,700 (GRCm39) |
I388T |
probably damaging |
Het |
| Sprn |
A |
C |
7: 139,733,469 (GRCm39) |
|
probably benign |
Het |
| Tango6 |
T |
C |
8: 107,426,863 (GRCm39) |
V459A |
possibly damaging |
Het |
| Tert |
C |
T |
13: 73,775,939 (GRCm39) |
T230I |
probably benign |
Het |
| Thada |
T |
C |
17: 84,733,614 (GRCm39) |
D1011G |
possibly damaging |
Het |
| Tln2 |
C |
T |
9: 67,302,743 (GRCm39) |
R76Q |
probably damaging |
Het |
| Trip11 |
A |
T |
12: 101,851,549 (GRCm39) |
N838K |
possibly damaging |
Het |
| Ttn |
A |
G |
2: 76,597,997 (GRCm39) |
W19639R |
probably damaging |
Het |
| Ubr4 |
T |
A |
4: 139,135,983 (GRCm39) |
S924T |
probably benign |
Het |
| Upb1 |
A |
G |
10: 75,250,861 (GRCm39) |
E110G |
probably benign |
Het |
| Vegfa |
C |
T |
17: 46,339,272 (GRCm39) |
|
probably null |
Het |
| Vmn1r231 |
T |
C |
17: 21,110,901 (GRCm39) |
K5E |
possibly damaging |
Het |
| Vmn2r16 |
A |
T |
5: 109,487,168 (GRCm39) |
I130F |
probably benign |
Het |
| Wscd2 |
T |
A |
5: 113,689,240 (GRCm39) |
V82E |
probably benign |
Het |
| Zfp462 |
A |
G |
4: 55,008,612 (GRCm39) |
T193A |
probably benign |
Het |
| Zfp467 |
A |
G |
6: 48,416,291 (GRCm39) |
|
probably benign |
Het |
| Zfp619 |
T |
C |
7: 39,186,412 (GRCm39) |
L814P |
probably benign |
Het |
|
| Other mutations in Nphp3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
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'- ATACATGTCTGTGTGCACATGC -3'
(R):5'- CCAGAACTGAGATGGCACTG -3'
Sequencing Primer
(F):5'- ACACACCGGTACTTCACTGTGG -3'
(R):5'- GCACTGCCACCATTGCG -3'
|
| Posted On |
2015-10-21 |
Incidental Mutation