Incidental Mutation 'R6890:Nphp3'
| ID |
537159 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nphp3
|
| Ensembl Gene |
ENSMUSG00000032558 |
| Gene Name |
nephronophthisis 3 (adolescent) |
| Synonyms |
pcy, 3632410F03Rik, D330020E01Rik, nephrocystin 3 |
| MMRRC Submission |
044984-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6890 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
103879743-103921010 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 103919153 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Serine
at position 1267
(Y1267S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000035167
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000035166]
[ENSMUST00000035167]
[ENSMUST00000193439]
[ENSMUST00000194183]
[ENSMUST00000194774]
[ENSMUST00000216593]
|
| AlphaFold |
Q7TNH6 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000035166
|
| SMART Domains |
Protein: ENSMUSP00000035166
Gene: ENSMUSG00000032557
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
1 |
30 |
N/A |
INTRINSIC |
|
Pfam:ThiF
|
51 |
309 |
2.8e-48 |
PFAM |
|
low complexity region
|
317 |
332 |
N/A |
INTRINSIC |
|
low complexity region
|
343 |
353 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000035167
AA Change: Y1267S
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000035167
Gene: ENSMUSG00000032558
AA Change: Y1267S
| 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 |
probably benign
Transcript: ENSMUST00000147249
|
| SMART Domains |
Protein: ENSMUSP00000115381
Gene: ENSMUSG00000101152
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
probably benign
Transcript: ENSMUST00000193439
|
| SMART Domains |
Protein: ENSMUSP00000141540
Gene: ENSMUSG00000032558
| 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: ENSMUST00000194183
|
| SMART Domains |
Protein: ENSMUSP00000142049
Gene: ENSMUSG00000032558
| Domain | Start | End | E-Value | Type |
|---|
|
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: Y1147S
|
| SMART Domains |
Protein: ENSMUSP00000141596
Gene: ENSMUSG00000032558
AA Change: Y1147S
| 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 |
|
| Predicted Effect |
silent
Transcript: ENSMUST00000216593
|
| Meta Mutation Damage Score |
0.6037 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.4%
- 20x: 98.0%
|
| Validation Efficiency |
100% (39/39) |
| 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: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Alg3 |
T |
C |
16: 20,424,736 (GRCm39) |
T270A |
possibly damaging |
Het |
| Ambp |
G |
C |
4: 63,068,596 (GRCm39) |
H140Q |
probably benign |
Het |
| Arhgef10 |
T |
C |
8: 14,978,786 (GRCm39) |
C18R |
probably benign |
Het |
| Arhgef10l |
A |
G |
4: 140,271,730 (GRCm39) |
F548S |
probably damaging |
Het |
| Armh3 |
A |
G |
19: 45,948,796 (GRCm39) |
Y228H |
probably damaging |
Het |
| Cdhr1 |
T |
C |
14: 36,807,602 (GRCm39) |
D346G |
probably damaging |
Het |
| Col18a1 |
T |
A |
10: 76,949,318 (GRCm39) |
|
probably benign |
Het |
| Col1a2 |
T |
A |
6: 4,539,587 (GRCm39) |
L1285Q |
unknown |
Het |
| Cspg5 |
T |
C |
9: 110,075,852 (GRCm39) |
L196P |
probably damaging |
Het |
| Dusp10 |
T |
G |
1: 183,801,393 (GRCm39) |
Y387D |
probably damaging |
Het |
| Epb41 |
A |
T |
4: 131,663,140 (GRCm39) |
D681E |
probably damaging |
Het |
| Eps8 |
A |
G |
6: 137,489,255 (GRCm39) |
V381A |
probably damaging |
Het |
| Fbxw16 |
A |
T |
9: 109,265,810 (GRCm39) |
S336R |
probably benign |
Het |
| Gm49368 |
A |
G |
7: 127,680,901 (GRCm39) |
R277G |
probably benign |
Het |
| Gsg1 |
C |
T |
6: 135,214,418 (GRCm39) |
V320I |
probably benign |
Het |
| Iglc3 |
T |
A |
16: 18,884,258 (GRCm39) |
|
probably benign |
Het |
| Klc4 |
A |
T |
17: 46,942,769 (GRCm39) |
N598K |
probably benign |
Het |
| Malsu1 |
A |
G |
6: 49,052,185 (GRCm39) |
Y135C |
probably damaging |
Het |
| Mapkbp1 |
T |
C |
2: 119,846,283 (GRCm39) |
I477T |
probably damaging |
Het |
| Mtss1 |
G |
T |
15: 58,823,508 (GRCm39) |
S286R |
probably damaging |
Het |
| Naip2 |
A |
C |
13: 100,298,549 (GRCm39) |
S496A |
probably benign |
Het |
| Niban3 |
T |
A |
8: 72,058,315 (GRCm39) |
V540D |
probably damaging |
Het |
| Npepps |
A |
T |
11: 97,158,470 (GRCm39) |
C98* |
probably null |
Het |
| Npr3 |
A |
G |
15: 11,883,478 (GRCm39) |
V317A |
possibly damaging |
Het |
| Nsun6 |
A |
G |
2: 15,053,788 (GRCm39) |
I7T |
probably damaging |
Het |
| Or13p4 |
A |
G |
4: 118,546,728 (GRCm39) |
V307A |
possibly damaging |
Het |
| Or51ai2 |
A |
T |
7: 103,587,066 (GRCm39) |
T160S |
possibly damaging |
Het |
| Or5b121 |
C |
T |
19: 13,507,445 (GRCm39) |
T180I |
probably damaging |
Het |
| Pcnx1 |
A |
G |
12: 82,018,150 (GRCm39) |
H1330R |
probably benign |
Het |
| Rad17 |
T |
C |
13: 100,773,592 (GRCm39) |
I201V |
probably benign |
Het |
| Slc26a4 |
G |
A |
12: 31,599,950 (GRCm39) |
T126M |
possibly damaging |
Het |
| Slitrk6 |
A |
T |
14: 110,988,528 (GRCm39) |
L393* |
probably null |
Het |
| Snx2 |
A |
G |
18: 53,345,951 (GRCm39) |
H378R |
probably damaging |
Het |
| Tex21 |
A |
G |
12: 76,286,229 (GRCm39) |
|
probably null |
Het |
| Trio |
A |
T |
15: 27,919,374 (GRCm39) |
|
probably benign |
Het |
| Vpreb1b |
T |
C |
16: 17,798,820 (GRCm39) |
I102T |
probably damaging |
Het |
| Zfp617 |
T |
G |
8: 72,686,010 (GRCm39) |
H113Q |
probably benign |
Het |
| Zgpat |
T |
A |
2: 181,020,304 (GRCm39) |
I237N |
probably damaging |
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 |
|
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 |
|
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'- GCAGGTGATAACAACACTTAGC -3'
(R):5'- TTGACGGTTAGCTTTGCCC -3'
Sequencing Primer
(F):5'- TTTCTTAAATACAGGGGAACACCAGG -3'
(R):5'- CCTTGGGGAAGAAAAACGTTAG -3'
|
| Posted On |
2018-10-18 |
Incidental Mutation