Incidental Mutation 'R2926:Nphp4'
| ID |
255749 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nphp4
|
| Ensembl Gene |
ENSMUSG00000039577 |
| Gene Name |
nephronophthisis 4 (juvenile) homolog (human) |
| Synonyms |
nmf192, 4930564O18Rik |
| MMRRC Submission |
040511-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.133)
|
| Stock # |
R2926 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
152561163-152647640 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 152602596 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 390
(V390A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000080128
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056567]
[ENSMUST00000081393]
|
| AlphaFold |
P59240 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000056567
AA Change: V390A
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000049920
Gene: ENSMUSG00000039577
AA Change: V390A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
317 |
333 |
N/A |
INTRINSIC |
|
low complexity region
|
367 |
380 |
N/A |
INTRINSIC |
|
low complexity region
|
473 |
484 |
N/A |
INTRINSIC |
|
low complexity region
|
507 |
530 |
N/A |
INTRINSIC |
|
low complexity region
|
896 |
909 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000081393
AA Change: V390A
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000080128
Gene: ENSMUSG00000039577
AA Change: V390A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
317 |
333 |
N/A |
INTRINSIC |
|
low complexity region
|
367 |
380 |
N/A |
INTRINSIC |
|
low complexity region
|
473 |
484 |
N/A |
INTRINSIC |
|
low complexity region
|
507 |
530 |
N/A |
INTRINSIC |
|
low complexity region
|
896 |
909 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123635
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000142027
|
| Meta Mutation Damage Score |
0.2048 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.3%
|
| Validation Efficiency |
98% (50/51) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal disease, and with Senior-Loken syndrome type 4, a combination of nephronophthisis and retinitis pigmentosa. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mutant mice have a mottled retina with photoreceptor degeneration and male infertility associated with oligozoospermia and asthenozoospermia. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb9 |
G |
T |
5: 124,216,902 (GRCm39) |
S438R |
possibly damaging |
Het |
| Add3 |
A |
G |
19: 53,215,253 (GRCm39) |
|
probably null |
Het |
| Adgrb2 |
T |
C |
4: 129,902,137 (GRCm39) |
L506P |
probably damaging |
Het |
| Atp6v0a1 |
A |
T |
11: 100,934,774 (GRCm39) |
I621L |
probably damaging |
Het |
| Calb1 |
T |
G |
4: 15,904,302 (GRCm39) |
L218R |
probably damaging |
Het |
| Ccdc162 |
G |
A |
10: 41,437,203 (GRCm39) |
|
probably benign |
Het |
| Ccser2 |
A |
T |
14: 36,601,518 (GRCm39) |
S842T |
possibly damaging |
Het |
| Cd300a |
A |
G |
11: 114,784,139 (GRCm39) |
E49G |
possibly damaging |
Het |
| Colec11 |
T |
A |
12: 28,667,428 (GRCm39) |
Q37L |
probably damaging |
Het |
| D630045J12Rik |
T |
A |
6: 38,145,106 (GRCm39) |
I1307F |
probably damaging |
Het |
| Dapk1 |
T |
C |
13: 60,867,564 (GRCm39) |
V257A |
possibly damaging |
Het |
| Dnah3 |
T |
A |
7: 119,550,338 (GRCm39) |
N3327I |
probably damaging |
Het |
| Gja8 |
C |
T |
3: 96,826,469 (GRCm39) |
V398I |
probably benign |
Het |
| Hfm1 |
A |
T |
5: 107,022,148 (GRCm39) |
L179* |
probably null |
Het |
| Hsd3b9 |
A |
G |
3: 98,357,872 (GRCm39) |
|
probably benign |
Het |
| Ift88 |
T |
C |
14: 57,726,375 (GRCm39) |
Y678H |
probably damaging |
Het |
| Itga10 |
A |
G |
3: 96,560,165 (GRCm39) |
N560D |
probably damaging |
Het |
| Itpk1 |
G |
T |
12: 102,545,389 (GRCm39) |
P238Q |
probably damaging |
Het |
| Kl |
T |
C |
5: 150,876,806 (GRCm39) |
W209R |
probably damaging |
Het |
| Lama4 |
A |
G |
10: 38,954,828 (GRCm39) |
N1127S |
probably benign |
Het |
| Lrp1 |
C |
T |
10: 127,423,982 (GRCm39) |
C830Y |
probably damaging |
Het |
| Mcmbp |
G |
A |
7: 128,299,738 (GRCm39) |
|
probably benign |
Het |
| Mrps33 |
A |
G |
6: 39,782,438 (GRCm39) |
S28P |
probably damaging |
Het |
| Myo9b |
G |
A |
8: 71,786,981 (GRCm39) |
R721Q |
probably benign |
Het |
| Myt1 |
C |
T |
2: 181,467,803 (GRCm39) |
T1079M |
possibly damaging |
Het |
| N4bp1 |
A |
T |
8: 87,588,424 (GRCm39) |
Y171* |
probably null |
Het |
| Ncln |
G |
T |
10: 81,324,272 (GRCm39) |
T442K |
probably benign |
Het |
| Ntrk2 |
C |
A |
13: 59,208,098 (GRCm39) |
T648K |
probably damaging |
Het |
| Nwd1 |
A |
G |
8: 73,393,640 (GRCm39) |
H301R |
probably damaging |
Het |
| Or4k5 |
A |
T |
14: 50,385,893 (GRCm39) |
V146E |
probably benign |
Het |
| Pcdh12 |
T |
C |
18: 38,415,443 (GRCm39) |
N561D |
probably damaging |
Het |
| Pcnx1 |
T |
A |
12: 82,041,769 (GRCm39) |
S2134T |
probably damaging |
Het |
| Ppp1cc |
G |
A |
5: 122,312,151 (GRCm39) |
A306T |
probably benign |
Het |
| Pramel3e |
G |
T |
X: 134,400,297 (GRCm39) |
A96S |
possibly damaging |
Het |
| Prrc2c |
C |
T |
1: 162,533,696 (GRCm39) |
|
probably benign |
Het |
| Rabggta |
C |
T |
14: 55,956,747 (GRCm39) |
R319H |
probably benign |
Het |
| Scn10a |
A |
C |
9: 119,467,767 (GRCm39) |
F791C |
possibly damaging |
Het |
| Stab1 |
T |
A |
14: 30,883,756 (GRCm39) |
D267V |
probably damaging |
Het |
| Sva |
A |
T |
6: 42,019,596 (GRCm39) |
Y152F |
possibly damaging |
Het |
| Tgfbrap1 |
T |
G |
1: 43,114,789 (GRCm39) |
M104L |
probably damaging |
Het |
| Tmed4 |
T |
C |
11: 6,221,728 (GRCm39) |
T203A |
probably benign |
Het |
| Toe1 |
C |
T |
4: 116,662,177 (GRCm39) |
A331T |
possibly damaging |
Het |
| Trappc9 |
G |
A |
15: 72,897,816 (GRCm39) |
R377W |
probably damaging |
Het |
| Trpm7 |
T |
C |
2: 126,700,329 (GRCm39) |
|
probably benign |
Het |
| Ttll7 |
C |
T |
3: 146,636,170 (GRCm39) |
R438* |
probably null |
Het |
| Usp11 |
G |
T |
X: 20,584,031 (GRCm39) |
G601W |
probably damaging |
Het |
| Vmn2r112 |
A |
G |
17: 22,833,984 (GRCm39) |
T551A |
possibly damaging |
Het |
| Vmn2r73 |
T |
C |
7: 85,520,871 (GRCm39) |
K366E |
probably benign |
Het |
| Vps33a |
A |
G |
5: 123,707,634 (GRCm39) |
I111T |
possibly damaging |
Het |
|
| Other mutations in Nphp4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00922:Nphp4
|
APN |
4 |
152,621,766 (GRCm39) |
splice site |
probably benign |
|
|
IGL00963:Nphp4
|
APN |
4 |
152,622,318 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL01571:Nphp4
|
APN |
4 |
152,640,839 (GRCm39) |
missense |
probably benign |
0.21 |
|
IGL01707:Nphp4
|
APN |
4 |
152,623,440 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01837:Nphp4
|
APN |
4 |
152,573,338 (GRCm39) |
missense |
probably damaging |
0.96 |
|
IGL02341:Nphp4
|
APN |
4 |
152,639,926 (GRCm39) |
splice site |
probably benign |
|
|
IGL02558:Nphp4
|
APN |
4 |
152,639,988 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02563:Nphp4
|
APN |
4 |
152,640,677 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02712:Nphp4
|
APN |
4 |
152,640,732 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03023:Nphp4
|
APN |
4 |
152,608,692 (GRCm39) |
splice site |
probably null |
|
|
R0280:Nphp4
|
UTSW |
4 |
152,636,393 (GRCm39) |
splice site |
probably benign |
|
|
R0317:Nphp4
|
UTSW |
4 |
152,636,388 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0410:Nphp4
|
UTSW |
4 |
152,641,503 (GRCm39) |
missense |
probably benign |
|
|
R0433:Nphp4
|
UTSW |
4 |
152,602,629 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0706:Nphp4
|
UTSW |
4 |
152,640,074 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R0785:Nphp4
|
UTSW |
4 |
152,646,566 (GRCm39) |
missense |
possibly damaging |
0.58 |
|
R0890:Nphp4
|
UTSW |
4 |
152,582,677 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R0930:Nphp4
|
UTSW |
4 |
152,622,512 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1202:Nphp4
|
UTSW |
4 |
152,573,186 (GRCm39) |
splice site |
probably null |
|
|
R1203:Nphp4
|
UTSW |
4 |
152,573,289 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R1366:Nphp4
|
UTSW |
4 |
152,587,383 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R1452:Nphp4
|
UTSW |
4 |
152,631,475 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1598:Nphp4
|
UTSW |
4 |
152,646,547 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1699:Nphp4
|
UTSW |
4 |
152,581,121 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2007:Nphp4
|
UTSW |
4 |
152,639,111 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R2082:Nphp4
|
UTSW |
4 |
152,643,821 (GRCm39) |
missense |
probably benign |
0.38 |
|
R2264:Nphp4
|
UTSW |
4 |
152,587,465 (GRCm39) |
splice site |
probably benign |
|
|
R2280:Nphp4
|
UTSW |
4 |
152,641,500 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R2281:Nphp4
|
UTSW |
4 |
152,641,500 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R3764:Nphp4
|
UTSW |
4 |
152,622,474 (GRCm39) |
splice site |
probably benign |
|
|
R4084:Nphp4
|
UTSW |
4 |
152,573,248 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4091:Nphp4
|
UTSW |
4 |
152,631,475 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R4240:Nphp4
|
UTSW |
4 |
152,640,141 (GRCm39) |
missense |
probably benign |
0.07 |
|
R4701:Nphp4
|
UTSW |
4 |
152,581,116 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4778:Nphp4
|
UTSW |
4 |
152,640,748 (GRCm39) |
missense |
probably benign |
0.44 |
|
R4783:Nphp4
|
UTSW |
4 |
152,639,003 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4784:Nphp4
|
UTSW |
4 |
152,639,003 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4974:Nphp4
|
UTSW |
4 |
152,622,250 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5053:Nphp4
|
UTSW |
4 |
152,628,919 (GRCm39) |
splice site |
probably null |
|
|
R5117:Nphp4
|
UTSW |
4 |
152,608,689 (GRCm39) |
splice site |
probably null |
|
|
R5128:Nphp4
|
UTSW |
4 |
152,587,448 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5665:Nphp4
|
UTSW |
4 |
152,590,942 (GRCm39) |
missense |
probably benign |
0.25 |
|
R5890:Nphp4
|
UTSW |
4 |
152,631,536 (GRCm39) |
missense |
probably benign |
0.44 |
|
R6171:Nphp4
|
UTSW |
4 |
152,628,906 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6601:Nphp4
|
UTSW |
4 |
152,587,464 (GRCm39) |
splice site |
probably null |
|
|
R6772:Nphp4
|
UTSW |
4 |
152,628,863 (GRCm39) |
missense |
probably benign |
0.07 |
|
R6806:Nphp4
|
UTSW |
4 |
152,622,558 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7006:Nphp4
|
UTSW |
4 |
152,573,259 (GRCm39) |
missense |
probably benign |
0.12 |
|
R7124:Nphp4
|
UTSW |
4 |
152,640,141 (GRCm39) |
missense |
probably benign |
0.07 |
|
R7381:Nphp4
|
UTSW |
4 |
152,583,460 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7411:Nphp4
|
UTSW |
4 |
152,639,174 (GRCm39) |
missense |
probably benign |
0.25 |
|
R7638:Nphp4
|
UTSW |
4 |
152,638,991 (GRCm39) |
missense |
probably benign |
0.08 |
|
R7814:Nphp4
|
UTSW |
4 |
152,628,860 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7814:Nphp4
|
UTSW |
4 |
152,608,729 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R7841:Nphp4
|
UTSW |
4 |
152,581,140 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8346:Nphp4
|
UTSW |
4 |
152,645,778 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8479:Nphp4
|
UTSW |
4 |
152,608,747 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8847:Nphp4
|
UTSW |
4 |
152,590,863 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8995:Nphp4
|
UTSW |
4 |
152,623,345 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8997:Nphp4
|
UTSW |
4 |
152,623,345 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9075:Nphp4
|
UTSW |
4 |
152,591,905 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9089:Nphp4
|
UTSW |
4 |
152,645,673 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R9191:Nphp4
|
UTSW |
4 |
152,640,687 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9274:Nphp4
|
UTSW |
4 |
152,640,056 (GRCm39) |
missense |
probably benign |
0.05 |
|
R9311:Nphp4
|
UTSW |
4 |
152,608,714 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9383:Nphp4
|
UTSW |
4 |
152,628,918 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9628:Nphp4
|
UTSW |
4 |
152,568,966 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9711:Nphp4
|
UTSW |
4 |
152,623,434 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R9712:Nphp4
|
UTSW |
4 |
152,631,521 (GRCm39) |
missense |
probably benign |
0.17 |
|
R9752:Nphp4
|
UTSW |
4 |
152,621,737 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9790:Nphp4
|
UTSW |
4 |
152,646,605 (GRCm39) |
missense |
probably null |
0.64 |
|
R9791:Nphp4
|
UTSW |
4 |
152,646,605 (GRCm39) |
missense |
probably null |
0.64 |
|
T0970:Nphp4
|
UTSW |
4 |
152,640,836 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0058:Nphp4
|
UTSW |
4 |
152,644,164 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
Z1177:Nphp4
|
UTSW |
4 |
152,602,653 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GTGTCAGTAAAGGCTGTCCTCC -3'
(R):5'- GCATCTGAGAACCACACCTATG -3'
Sequencing Primer
(F):5'- CTGCTCTGAGCTCCTGGAATG -3'
(R):5'- ATGAAGTGCTTACCTCCTCGGAG -3'
|
| Posted On |
2014-12-29 |
Incidental Mutation