Incidental Mutation 'R4425:Nphp1'
| ID |
371077 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nphp1
|
| Ensembl Gene |
ENSMUSG00000027378 |
| Gene Name |
nephronophthisis 1 (juvenile) homolog (human) |
| Synonyms |
nephrocystin |
| MMRRC Submission |
041144-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4425 (G1)
|
| Quality Score |
73 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
127582652-127630817 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 127630719 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 19
(E19G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105986
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028857]
[ENSMUST00000110357]
[ENSMUST00000135091]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000028857
AA Change: E19G
PolyPhen 2
Score 0.819 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000028857
Gene: ENSMUSG00000027378
AA Change: E19G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
118 |
143 |
N/A |
INTRINSIC |
|
SH3
|
158 |
214 |
5.91e-19 |
SMART |
|
low complexity region
|
220 |
246 |
N/A |
INTRINSIC |
|
Blast:14_3_3
|
391 |
491 |
3e-55 |
BLAST |
|
low complexity region
|
634 |
641 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000110357
AA Change: E19G
PolyPhen 2
Score 0.819 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000105986
Gene: ENSMUSG00000027378
AA Change: E19G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
118 |
143 |
N/A |
INTRINSIC |
|
SH3
|
158 |
214 |
5.91e-19 |
SMART |
|
low complexity region
|
220 |
246 |
N/A |
INTRINSIC |
|
Blast:14_3_3
|
390 |
490 |
3e-55 |
BLAST |
|
low complexity region
|
633 |
640 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000135091
|
| SMART Domains |
Protein: ENSMUSP00000141107
Gene: ENSMUSG00000051319
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF1049
|
1 |
56 |
1.1e-9 |
PFAM |
|
| Meta Mutation Damage Score |
0.0794 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
| Validation Efficiency |
98% (55/56) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as part of a multifunctional complex localized in actin- and microtubule-based structures. Mutations in this gene cause familial juvenile nephronophthisis type 1, a kidney disorder involving both tubules and glomeruli. Defects in this gene are also associated with Senior-Loken syndrome type 1, also referred to as juvenile nephronophthisis with Leber amaurosis, which is characterized by kidney and eye disease, and with Joubert syndrome type 4, which is characterized by cerebellar ataxia, oculomotor apraxia, psychomotor delay and neonatal breathing abnormalities, sometimes including retinal dystrophy and renal disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit male infertility due to defects in sperm maturation. Mice homozygous for another knock-out allele exhibit absent photoreceptor outer segment and photoreceptor degeneration. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc3 |
T |
C |
11: 94,236,870 (GRCm39) |
T1456A |
probably damaging |
Het |
| Acad11 |
T |
C |
9: 103,950,844 (GRCm39) |
F56S |
probably damaging |
Het |
| Adamts8 |
A |
G |
9: 30,867,952 (GRCm39) |
N592S |
possibly damaging |
Het |
| Amh |
A |
G |
10: 80,642,755 (GRCm39) |
D313G |
probably damaging |
Het |
| Ampd2 |
T |
C |
3: 107,994,052 (GRCm39) |
|
probably benign |
Het |
| Arap3 |
A |
G |
18: 38,111,653 (GRCm39) |
L1115P |
probably damaging |
Het |
| Arfgap1 |
C |
A |
2: 180,622,869 (GRCm39) |
D327E |
probably benign |
Het |
| Capns2 |
T |
A |
8: 93,628,252 (GRCm39) |
I47N |
possibly damaging |
Het |
| Cd163 |
T |
C |
6: 124,304,862 (GRCm39) |
S1080P |
possibly damaging |
Het |
| Ceacam10 |
A |
T |
7: 24,480,433 (GRCm39) |
Y68F |
possibly damaging |
Het |
| Cep44 |
G |
A |
8: 56,991,652 (GRCm39) |
P317S |
probably benign |
Het |
| Cfh |
A |
T |
1: 140,028,613 (GRCm39) |
Y688* |
probably null |
Het |
| Chrnb1 |
A |
T |
11: 69,677,773 (GRCm39) |
S326R |
probably damaging |
Het |
| Cngb1 |
C |
T |
8: 96,026,344 (GRCm39) |
V25M |
probably damaging |
Het |
| Cyp2c50 |
A |
T |
19: 40,079,136 (GRCm39) |
N160Y |
possibly damaging |
Het |
| Dalrd3 |
T |
C |
9: 108,448,800 (GRCm39) |
|
probably benign |
Het |
| Eef1d |
C |
A |
15: 75,774,648 (GRCm39) |
S253I |
possibly damaging |
Het |
| Efl1 |
G |
A |
7: 82,412,491 (GRCm39) |
C960Y |
probably damaging |
Het |
| Elmo1 |
C |
G |
13: 20,784,382 (GRCm39) |
Y646* |
probably null |
Het |
| Epb41l2 |
C |
A |
10: 25,382,078 (GRCm39) |
D701E |
possibly damaging |
Het |
| Fbxl4 |
T |
A |
4: 22,422,699 (GRCm39) |
|
probably null |
Het |
| Fhod1 |
T |
C |
8: 106,063,983 (GRCm39) |
|
probably benign |
Het |
| Gm8741 |
G |
T |
17: 35,555,062 (GRCm39) |
|
noncoding transcript |
Het |
| Igkv10-95 |
A |
T |
6: 68,657,606 (GRCm39) |
I21F |
probably damaging |
Het |
| Il10rb |
C |
A |
16: 91,204,603 (GRCm39) |
N51K |
possibly damaging |
Het |
| Krt78 |
T |
C |
15: 101,856,375 (GRCm39) |
T479A |
probably benign |
Het |
| Lrig3 |
T |
C |
10: 125,849,273 (GRCm39) |
S998P |
probably benign |
Het |
| Lrrc8c |
T |
A |
5: 105,755,755 (GRCm39) |
M510K |
probably benign |
Het |
| Nfrkb |
G |
T |
9: 31,311,258 (GRCm39) |
C369F |
probably damaging |
Het |
| Or10a5 |
A |
C |
7: 106,635,698 (GRCm39) |
E112A |
probably damaging |
Het |
| Or4f14b |
T |
C |
2: 111,775,534 (GRCm39) |
H89R |
probably benign |
Het |
| Ovol3 |
A |
T |
7: 29,934,789 (GRCm39) |
|
probably null |
Het |
| Ppp1r16b |
C |
T |
2: 158,599,174 (GRCm39) |
T382I |
probably benign |
Het |
| Rims2 |
T |
C |
15: 39,301,320 (GRCm39) |
|
probably null |
Het |
| Sh3rf3 |
T |
C |
10: 58,919,398 (GRCm39) |
V505A |
probably benign |
Het |
| Shkbp1 |
T |
C |
7: 27,042,727 (GRCm39) |
N570S |
probably benign |
Het |
| Slc35f4 |
C |
T |
14: 49,556,307 (GRCm39) |
V149I |
possibly damaging |
Het |
| Snx27 |
A |
G |
3: 94,469,330 (GRCm39) |
F4L |
probably benign |
Het |
| Syvn1 |
C |
T |
19: 6,099,951 (GRCm39) |
|
probably benign |
Het |
| Tagap1 |
G |
A |
17: 7,223,511 (GRCm39) |
S395L |
probably benign |
Het |
| Tcstv2b |
C |
A |
13: 120,373,908 (GRCm39) |
L127F |
probably damaging |
Het |
| Tek |
A |
G |
4: 94,751,904 (GRCm39) |
T1014A |
probably damaging |
Het |
| Top2a |
A |
G |
11: 98,892,231 (GRCm39) |
I1077T |
probably benign |
Het |
| Tpo |
T |
C |
12: 30,154,015 (GRCm39) |
Y230C |
probably damaging |
Het |
| Trav12-2 |
A |
G |
14: 53,854,332 (GRCm39) |
Q102R |
possibly damaging |
Het |
| Ttn |
G |
A |
2: 76,733,430 (GRCm39) |
|
probably benign |
Het |
| Vmn1r183 |
A |
T |
7: 23,754,973 (GRCm39) |
I259F |
probably benign |
Het |
| Vmn1r228 |
T |
C |
17: 20,996,861 (GRCm39) |
E219G |
probably damaging |
Het |
| Vsig8 |
G |
T |
1: 172,390,714 (GRCm39) |
G254V |
probably damaging |
Het |
| Vwa8 |
A |
G |
14: 79,320,246 (GRCm39) |
I1086V |
probably benign |
Het |
| Zfp423 |
G |
A |
8: 88,509,601 (GRCm39) |
H123Y |
probably damaging |
Het |
| Zfp811 |
A |
T |
17: 33,016,521 (GRCm39) |
C506* |
probably null |
Het |
|
| Other mutations in Nphp1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00570:Nphp1
|
APN |
2 |
127,605,805 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL00589:Nphp1
|
APN |
2 |
127,605,769 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01143:Nphp1
|
APN |
2 |
127,622,056 (GRCm39) |
missense |
probably benign |
0.06 |
|
IGL01893:Nphp1
|
APN |
2 |
127,611,564 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01922:Nphp1
|
APN |
2 |
127,621,989 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL02123:Nphp1
|
APN |
2 |
127,595,969 (GRCm39) |
missense |
probably benign |
0.03 |
|
IGL02340:Nphp1
|
APN |
2 |
127,621,987 (GRCm39) |
nonsense |
probably null |
|
|
IGL02836:Nphp1
|
APN |
2 |
127,611,543 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03109:Nphp1
|
APN |
2 |
127,610,089 (GRCm39) |
critical splice donor site |
probably benign |
|
|
R1632:Nphp1
|
UTSW |
2 |
127,612,312 (GRCm39) |
missense |
probably benign |
0.32 |
|
R1857:Nphp1
|
UTSW |
2 |
127,612,296 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4514:Nphp1
|
UTSW |
2 |
127,590,007 (GRCm39) |
missense |
probably benign |
0.26 |
|
R4546:Nphp1
|
UTSW |
2 |
127,607,939 (GRCm39) |
splice site |
probably null |
|
|
R4580:Nphp1
|
UTSW |
2 |
127,610,089 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5634:Nphp1
|
UTSW |
2 |
127,601,570 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R7152:Nphp1
|
UTSW |
2 |
127,595,899 (GRCm39) |
missense |
probably benign |
|
|
R7326:Nphp1
|
UTSW |
2 |
127,603,137 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
R7985:Nphp1
|
UTSW |
2 |
127,587,829 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R8029:Nphp1
|
UTSW |
2 |
127,583,036 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8715:Nphp1
|
UTSW |
2 |
127,605,729 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R8967:Nphp1
|
UTSW |
2 |
127,582,897 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8997:Nphp1
|
UTSW |
2 |
127,595,982 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R9328:Nphp1
|
UTSW |
2 |
127,582,892 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R9450:Nphp1
|
UTSW |
2 |
127,616,008 (GRCm39) |
missense |
|
|
|
R9755:Nphp1
|
UTSW |
2 |
127,595,951 (GRCm39) |
nonsense |
probably null |
|
|
X0022:Nphp1
|
UTSW |
2 |
127,603,134 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0025:Nphp1
|
UTSW |
2 |
127,621,047 (GRCm39) |
missense |
probably benign |
0.16 |
|
| Predicted Primers |
PCR Primer
(F):5'- CGTTGACACCTGTTACACTTTG -3'
(R):5'- TTAGTGCAACCTGTGGCACG -3'
Sequencing Primer
(F):5'- CTGGCTAGTTTAGACAAGGGCC -3'
(R):5'- CCTGTGGCACGGGGTTG -3'
|
| Posted On |
2016-02-16 |
Incidental Mutation