Incidental Mutation 'R3151:Nphs1'
| ID |
264403 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nphs1
|
| Ensembl Gene |
ENSMUSG00000006649 |
| Gene Name |
nephrosis 1, nephrin |
| Synonyms |
nephrin |
| MMRRC Submission |
040603-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R3151 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
30157740-30186648 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 30159665 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Serine
at position 33
(T33S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000006825
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006825]
[ENSMUST00000045817]
[ENSMUST00000126297]
|
| AlphaFold |
Q9QZS7 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000006825
AA Change: T33S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000006825
Gene: ENSMUSG00000006649
AA Change: T33S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
36 |
N/A |
INTRINSIC |
|
IG
|
52 |
146 |
1.38e-6 |
SMART |
|
Pfam:C2-set_2
|
152 |
242 |
4.1e-20 |
PFAM |
|
IG
|
264 |
351 |
9.86e-3 |
SMART |
|
IG_like
|
360 |
452 |
2.73e1 |
SMART |
|
IG
|
464 |
556 |
2.99e-2 |
SMART |
|
IG_like
|
572 |
644 |
8.9e-1 |
SMART |
|
IG
|
667 |
751 |
1.32e-3 |
SMART |
|
IG
|
760 |
849 |
7.3e-6 |
SMART |
|
IGc2
|
868 |
941 |
5.4e-9 |
SMART |
|
FN3
|
955 |
1036 |
1.01e-11 |
SMART |
|
transmembrane domain
|
1078 |
1100 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000045817
|
| SMART Domains |
Protein: ENSMUSP00000039395
Gene: ENSMUSG00000036915
| Domain | Start | End | E-Value | Type |
|---|
|
IG
|
27 |
117 |
9.18e-12 |
SMART |
|
IG
|
128 |
219 |
5.13e-1 |
SMART |
|
IG_like
|
230 |
306 |
8.06e0 |
SMART |
|
IGc2
|
321 |
379 |
3.06e-8 |
SMART |
|
IG_like
|
401 |
500 |
4.65e1 |
SMART |
|
transmembrane domain
|
509 |
531 |
N/A |
INTRINSIC |
|
low complexity region
|
547 |
565 |
N/A |
INTRINSIC |
|
low complexity region
|
607 |
629 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000117923
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000126297
|
| SMART Domains |
Protein: ENSMUSP00000116500
Gene: ENSMUSG00000006649
| Domain | Start | End | E-Value | Type |
|---|
|
IG
|
38 |
132 |
1.38e-6 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140565
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152625
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169893
|
| SMART Domains |
Protein: ENSMUSP00000131161
Gene: ENSMUSG00000036915
| Domain | Start | End | E-Value | Type |
|---|
|
IG
|
27 |
117 |
9.18e-12 |
SMART |
|
IG_like
|
118 |
189 |
5.91e-1 |
SMART |
|
IG_like
|
211 |
287 |
8.06e0 |
SMART |
|
IGc2
|
302 |
360 |
3.06e-8 |
SMART |
|
IG_like
|
382 |
481 |
4.65e1 |
SMART |
|
transmembrane domain
|
490 |
512 |
N/A |
INTRINSIC |
|
low complexity region
|
528 |
546 |
N/A |
INTRINSIC |
|
low complexity region
|
588 |
610 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.0%
|
| Validation Efficiency |
98% (61/62) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the immunoglobulin family of cell adhesion molecules that functions in the glomerular filtration barrier in the kidney. The gene is primarily expressed in renal tissues, and the protein is a type-1 transmembrane protein found at the slit diaphragm of glomerular podocytes. The slit diaphragm is thought to function as an ultrafilter to exclude albumin and other plasma macromolecules in the formation of urine. Mutations in this gene result in Finnish-type congenital nephrosis 1, characterized by severe proteinuria and loss of the slit diaphragm and foot processes.[provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit severe proteinuria associated with kidney defects and die soon after birth. Heterozygotes exhibit fusion of one-third of glomerular foot processes. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam5 |
A |
G |
8: 25,271,647 (GRCm39) |
Y587H |
probably damaging |
Het |
| Ahnak |
T |
C |
19: 8,987,308 (GRCm39) |
V2864A |
probably benign |
Het |
| Ano2 |
G |
A |
6: 125,990,280 (GRCm39) |
|
probably null |
Het |
| Arl5c |
A |
G |
11: 97,883,159 (GRCm39) |
I147T |
probably damaging |
Het |
| Asap2 |
T |
A |
12: 21,274,378 (GRCm39) |
F369I |
probably damaging |
Het |
| Atg4a-ps |
A |
G |
3: 103,553,228 (GRCm39) |
F38L |
probably benign |
Het |
| B230217C12Rik |
TGTGTCG |
TG |
11: 97,733,014 (GRCm39) |
|
probably null |
Het |
| Cacna1s |
A |
T |
1: 136,033,532 (GRCm39) |
Y1003F |
probably damaging |
Het |
| Ccdc178 |
A |
T |
18: 21,944,618 (GRCm39) |
M847K |
probably benign |
Het |
| Clca4b |
T |
C |
3: 144,621,272 (GRCm39) |
K601E |
probably benign |
Het |
| Cnih4 |
A |
G |
1: 180,981,292 (GRCm39) |
|
probably benign |
Het |
| Cnpy3 |
A |
T |
17: 47,058,452 (GRCm39) |
V57E |
probably damaging |
Het |
| Creb3l1 |
T |
A |
2: 91,832,378 (GRCm39) |
E48V |
probably damaging |
Het |
| Dus3l |
T |
A |
17: 57,075,899 (GRCm39) |
F482I |
probably benign |
Het |
| Dync1i2 |
A |
G |
2: 71,064,060 (GRCm39) |
|
probably benign |
Het |
| Echdc1 |
A |
G |
10: 29,198,360 (GRCm39) |
T102A |
possibly damaging |
Het |
| Elf1 |
G |
A |
14: 79,804,755 (GRCm39) |
|
probably null |
Het |
| Elp1 |
T |
C |
4: 56,770,985 (GRCm39) |
Y986C |
probably benign |
Het |
| Ep400 |
G |
T |
5: 110,851,435 (GRCm39) |
T1349N |
unknown |
Het |
| Eps15 |
T |
A |
4: 109,223,419 (GRCm39) |
D458E |
probably benign |
Het |
| F2rl2 |
G |
A |
13: 95,837,638 (GRCm39) |
V228I |
probably benign |
Het |
| Fads3 |
T |
G |
19: 10,035,262 (GRCm39) |
S438A |
probably benign |
Het |
| Fcgbp |
T |
A |
7: 27,816,665 (GRCm39) |
C2376S |
probably damaging |
Het |
| Fndc3b |
A |
G |
3: 27,473,652 (GRCm39) |
S1138P |
possibly damaging |
Het |
| Ggt5 |
T |
C |
10: 75,445,076 (GRCm39) |
I361T |
probably benign |
Het |
| Gpr158 |
C |
T |
2: 21,581,771 (GRCm39) |
R417W |
possibly damaging |
Het |
| Gria1 |
A |
G |
11: 57,174,388 (GRCm39) |
I626V |
probably damaging |
Het |
| Gys2 |
T |
C |
6: 142,402,059 (GRCm39) |
E260G |
probably benign |
Het |
| Ido2 |
T |
A |
8: 25,023,776 (GRCm39) |
Y354F |
possibly damaging |
Het |
| Igkv6-23 |
A |
G |
6: 70,237,543 (GRCm39) |
L66P |
probably benign |
Het |
| Kremen1 |
T |
C |
11: 5,145,012 (GRCm39) |
K455E |
probably damaging |
Het |
| Krtap19-9b |
T |
C |
16: 88,729,096 (GRCm39) |
S2G |
unknown |
Het |
| Magea1 |
A |
T |
X: 153,872,093 (GRCm39) |
M211K |
probably benign |
Het |
| Mtx2 |
G |
A |
2: 74,677,634 (GRCm39) |
|
probably null |
Het |
| Nlrp14 |
G |
A |
7: 106,781,759 (GRCm39) |
V319I |
probably benign |
Het |
| Or12j2 |
A |
T |
7: 139,916,243 (GRCm39) |
H156L |
probably benign |
Het |
| Or2t6 |
T |
A |
14: 14,175,203 (GRCm38) |
N293I |
probably damaging |
Het |
| Or3a1c |
A |
T |
11: 74,046,466 (GRCm39) |
H162L |
probably damaging |
Het |
| P2rx7 |
A |
G |
5: 122,819,329 (GRCm39) |
T584A |
probably benign |
Het |
| Pclo |
A |
G |
5: 14,571,692 (GRCm39) |
Q359R |
probably damaging |
Het |
| Phtf2 |
T |
C |
5: 20,970,802 (GRCm39) |
E147G |
probably damaging |
Het |
| Ptges2 |
G |
A |
2: 32,286,488 (GRCm39) |
A68T |
probably benign |
Het |
| Rab33b |
A |
T |
3: 51,401,069 (GRCm39) |
N181I |
possibly damaging |
Het |
| Rnf213 |
A |
T |
11: 119,359,718 (GRCm39) |
R4370S |
probably benign |
Het |
| Rpf1 |
G |
A |
3: 146,213,390 (GRCm39) |
R254W |
probably damaging |
Het |
| Serpinb7 |
A |
T |
1: 107,363,081 (GRCm39) |
R82* |
probably null |
Het |
| Setbp1 |
A |
G |
18: 78,900,650 (GRCm39) |
S1006P |
probably damaging |
Het |
| Spata31d1a |
T |
C |
13: 59,849,180 (GRCm39) |
S983G |
probably benign |
Het |
| Ssr2 |
T |
C |
3: 88,487,323 (GRCm39) |
I46T |
probably damaging |
Het |
| Ssx2ip |
G |
A |
3: 146,124,138 (GRCm39) |
G51D |
probably benign |
Het |
| Synj1 |
A |
T |
16: 90,757,514 (GRCm39) |
L878H |
probably damaging |
Het |
| Th |
G |
A |
7: 142,447,812 (GRCm39) |
Q329* |
probably null |
Het |
| Tln2 |
C |
T |
9: 67,237,829 (GRCm39) |
|
probably null |
Het |
| Trio |
A |
G |
15: 27,805,862 (GRCm39) |
L542P |
probably damaging |
Het |
| Trp53bp2 |
A |
G |
1: 182,256,525 (GRCm39) |
T32A |
probably damaging |
Het |
| Vmn1r40 |
A |
T |
6: 89,691,548 (GRCm39) |
T122S |
probably benign |
Het |
| Vmn2r121 |
C |
T |
X: 123,040,849 (GRCm39) |
C494Y |
probably benign |
Het |
| Vmn2r51 |
A |
T |
7: 9,833,968 (GRCm39) |
Y357N |
probably damaging |
Het |
| Vmn2r55 |
G |
T |
7: 12,404,634 (GRCm39) |
S256R |
probably benign |
Het |
| Vps8 |
A |
G |
16: 21,261,123 (GRCm39) |
T88A |
probably benign |
Het |
| Zfp977 |
A |
C |
7: 42,229,870 (GRCm39) |
N218K |
probably benign |
Het |
|
| Other mutations in Nphs1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00160:Nphs1
|
APN |
7 |
30,181,976 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
IGL00927:Nphs1
|
APN |
7 |
30,160,164 (GRCm39) |
unclassified |
probably benign |
|
|
IGL00976:Nphs1
|
APN |
7 |
30,160,110 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
IGL01397:Nphs1
|
APN |
7 |
30,186,089 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL01465:Nphs1
|
APN |
7 |
30,186,139 (GRCm39) |
makesense |
probably null |
|
|
IGL01889:Nphs1
|
APN |
7 |
30,159,936 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02383:Nphs1
|
APN |
7 |
30,181,060 (GRCm39) |
splice site |
probably benign |
|
|
R0020:Nphs1
|
UTSW |
7 |
30,162,633 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0485:Nphs1
|
UTSW |
7 |
30,166,940 (GRCm39) |
missense |
probably benign |
|
|
R1024:Nphs1
|
UTSW |
7 |
30,173,702 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1115:Nphs1
|
UTSW |
7 |
30,180,803 (GRCm39) |
splice site |
probably benign |
|
|
R1144:Nphs1
|
UTSW |
7 |
30,181,103 (GRCm39) |
splice site |
probably benign |
|
|
R1289:Nphs1
|
UTSW |
7 |
30,170,603 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1317:Nphs1
|
UTSW |
7 |
30,181,256 (GRCm39) |
splice site |
probably benign |
|
|
R1617:Nphs1
|
UTSW |
7 |
30,181,956 (GRCm39) |
missense |
probably benign |
|
|
R1756:Nphs1
|
UTSW |
7 |
30,160,959 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1937:Nphs1
|
UTSW |
7 |
30,173,798 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2144:Nphs1
|
UTSW |
7 |
30,160,395 (GRCm39) |
missense |
probably benign |
0.13 |
|
R2256:Nphs1
|
UTSW |
7 |
30,167,417 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R2257:Nphs1
|
UTSW |
7 |
30,167,417 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R2277:Nphs1
|
UTSW |
7 |
30,166,989 (GRCm39) |
nonsense |
probably null |
|
|
R3104:Nphs1
|
UTSW |
7 |
30,166,965 (GRCm39) |
nonsense |
probably null |
|
|
R3106:Nphs1
|
UTSW |
7 |
30,166,965 (GRCm39) |
nonsense |
probably null |
|
|
R3765:Nphs1
|
UTSW |
7 |
30,170,635 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4078:Nphs1
|
UTSW |
7 |
30,166,945 (GRCm39) |
nonsense |
probably null |
|
|
R4397:Nphs1
|
UTSW |
7 |
30,181,390 (GRCm39) |
splice site |
probably null |
|
|
R4635:Nphs1
|
UTSW |
7 |
30,167,432 (GRCm39) |
missense |
probably benign |
0.39 |
|
R4650:Nphs1
|
UTSW |
7 |
30,181,895 (GRCm39) |
missense |
probably benign |
0.21 |
|
R4811:Nphs1
|
UTSW |
7 |
30,159,854 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4850:Nphs1
|
UTSW |
7 |
30,162,657 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
R5272:Nphs1
|
UTSW |
7 |
30,181,067 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R5327:Nphs1
|
UTSW |
7 |
30,163,250 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5681:Nphs1
|
UTSW |
7 |
30,186,050 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5865:Nphs1
|
UTSW |
7 |
30,173,810 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5975:Nphs1
|
UTSW |
7 |
30,165,540 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R6186:Nphs1
|
UTSW |
7 |
30,165,059 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6198:Nphs1
|
UTSW |
7 |
30,167,340 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R6353:Nphs1
|
UTSW |
7 |
30,173,969 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7405:Nphs1
|
UTSW |
7 |
30,162,253 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R7647:Nphs1
|
UTSW |
7 |
30,181,390 (GRCm39) |
splice site |
probably null |
|
|
R7767:Nphs1
|
UTSW |
7 |
30,162,733 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8132:Nphs1
|
UTSW |
7 |
30,181,478 (GRCm39) |
missense |
probably benign |
0.02 |
|
R8485:Nphs1
|
UTSW |
7 |
30,165,598 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8678:Nphs1
|
UTSW |
7 |
30,163,284 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8890:Nphs1
|
UTSW |
7 |
30,162,080 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8946:Nphs1
|
UTSW |
7 |
30,162,625 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9133:Nphs1
|
UTSW |
7 |
30,160,092 (GRCm39) |
nonsense |
probably null |
|
|
R9159:Nphs1
|
UTSW |
7 |
30,165,026 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R9347:Nphs1
|
UTSW |
7 |
30,170,594 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9547:Nphs1
|
UTSW |
7 |
30,180,875 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9548:Nphs1
|
UTSW |
7 |
30,180,875 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9607:Nphs1
|
UTSW |
7 |
30,163,012 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9626:Nphs1
|
UTSW |
7 |
30,166,991 (GRCm39) |
missense |
probably benign |
0.16 |
|
R9720:Nphs1
|
UTSW |
7 |
30,165,499 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R9733:Nphs1
|
UTSW |
7 |
30,166,955 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0028:Nphs1
|
UTSW |
7 |
30,166,929 (GRCm39) |
missense |
probably null |
0.01 |
|
Z1177:Nphs1
|
UTSW |
7 |
30,170,328 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1186:Nphs1
|
UTSW |
7 |
30,159,775 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTTGGGGTTAGAGCTCAGAG -3'
(R):5'- AGCTTAACTGTCGACCCTTC -3'
Sequencing Primer
(F):5'- CTGCGACAGTCACAGACAATGG -3'
(R):5'- TCCACCACAGTCAGGTTTTCAGATAG -3'
|
| Posted On |
2015-02-05 |
Incidental Mutation