Incidental Mutation 'PIT4382001:Kdm3b'
| ID |
554727 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm3b
|
| Ensembl Gene |
ENSMUSG00000038773 |
| Gene Name |
KDM3B lysine (K)-specific demethylase 3B |
| Synonyms |
Jmjd1b, 5830462I21Rik, JHDM2B |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.940)
|
| Stock # |
PIT4382001 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
34910100-34971713 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 34942140 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 744
(S744P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000037628
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043775]
[ENSMUST00000224715]
[ENSMUST00000225195]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000043775
AA Change: S744P
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000037628
Gene: ENSMUSG00000038773
AA Change: S744P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
20 |
36 |
N/A |
INTRINSIC |
|
Blast:JmjC
|
149 |
944 |
N/A |
BLAST |
|
Blast:JmjC
|
946 |
1064 |
5e-40 |
BLAST |
|
Blast:JmjC
|
1069 |
1471 |
N/A |
BLAST |
|
JmjC
|
1499 |
1722 |
2.43e-65 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000224715
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000225195
AA Change: S544P
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| Coding Region Coverage |
- 1x: 92.9%
- 3x: 90.5%
- 10x: 84.6%
- 20x: 72.3%
|
| Validation Efficiency |
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 68 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9430038I01Rik |
G |
T |
7: 136,978,711 (GRCm39) |
H144N |
unknown |
Het |
| Acsm4 |
C |
T |
7: 119,297,798 (GRCm39) |
T145M |
probably damaging |
Het |
| Adam10 |
T |
C |
9: 70,673,363 (GRCm39) |
L498P |
probably damaging |
Het |
| Adgrl2 |
A |
G |
3: 148,522,934 (GRCm39) |
L430P |
|
Het |
| Alk |
T |
C |
17: 72,256,916 (GRCm39) |
M648V |
probably benign |
Het |
| Arhgap35 |
T |
C |
7: 16,297,794 (GRCm39) |
R424G |
possibly damaging |
Het |
| Baiap2l1 |
T |
C |
5: 144,215,480 (GRCm39) |
K342E |
possibly damaging |
Het |
| Ccdc54 |
C |
T |
16: 50,411,219 (GRCm39) |
V16M |
probably damaging |
Het |
| Chil3 |
T |
G |
3: 106,055,975 (GRCm39) |
D366A |
probably damaging |
Het |
| Chuk |
A |
G |
19: 44,087,046 (GRCm39) |
V151A |
probably damaging |
Het |
| Cpd |
T |
G |
11: 76,688,614 (GRCm39) |
H886P |
probably benign |
Het |
| Cped1 |
T |
A |
6: 22,222,449 (GRCm39) |
C736* |
probably null |
Het |
| Creb3l3 |
T |
C |
10: 80,920,746 (GRCm39) |
E428G |
probably benign |
Het |
| Csad |
G |
A |
15: 102,097,085 (GRCm39) |
L7F |
probably benign |
Het |
| Dnah1 |
C |
T |
14: 31,006,412 (GRCm39) |
D2255N |
probably damaging |
Het |
| Dnajb12 |
T |
C |
10: 59,728,508 (GRCm39) |
Y159H |
probably damaging |
Het |
| Dpysl4 |
T |
A |
7: 138,669,494 (GRCm39) |
Y57* |
probably null |
Het |
| F2rl1 |
T |
G |
13: 95,650,154 (GRCm39) |
N243H |
probably benign |
Het |
| Fhl4 |
T |
C |
10: 84,934,293 (GRCm39) |
K163E |
possibly damaging |
Het |
| Flot2 |
T |
C |
11: 77,944,193 (GRCm39) |
S46P |
possibly damaging |
Het |
| Fsip2 |
C |
A |
2: 82,821,196 (GRCm39) |
T5643K |
possibly damaging |
Het |
| Golga4 |
T |
A |
9: 118,382,521 (GRCm39) |
Y542N |
possibly damaging |
Het |
| Il17re |
A |
G |
6: 113,446,038 (GRCm39) |
T426A |
probably benign |
Het |
| Kdm2a |
T |
A |
19: 4,393,201 (GRCm39) |
M385L |
probably benign |
Het |
| Krtap20-1 |
T |
A |
16: 88,881,048 (GRCm39) |
Y26* |
probably null |
Het |
| Lama2 |
T |
C |
10: 27,080,901 (GRCm39) |
D974G |
probably damaging |
Het |
| Ldc1 |
A |
T |
4: 130,112,954 (GRCm39) |
N147K |
possibly damaging |
Het |
| Lipo5 |
A |
T |
19: 33,443,339 (GRCm39) |
L159Q |
probably null |
Het |
| LTO1 |
T |
A |
7: 144,470,181 (GRCm39) |
Y37N |
probably damaging |
Het |
| Mau2 |
C |
T |
8: 70,483,302 (GRCm39) |
E187K |
possibly damaging |
Het |
| Mrpl9 |
T |
C |
3: 94,355,136 (GRCm39) |
L236P |
probably benign |
Het |
| Mta1 |
A |
G |
12: 113,096,870 (GRCm39) |
T564A |
probably benign |
Het |
| Mylk |
C |
T |
16: 34,696,012 (GRCm39) |
S249L |
probably damaging |
Het |
| Ncor1 |
G |
T |
11: 62,235,489 (GRCm39) |
T331K |
probably damaging |
Het |
| Nsun3 |
T |
A |
16: 62,606,228 (GRCm39) |
K15N |
probably damaging |
Het |
| Nsun5 |
A |
G |
5: 135,400,355 (GRCm39) |
Y132C |
probably benign |
Het |
| Obsl1 |
T |
A |
1: 75,464,607 (GRCm39) |
T1605S |
probably benign |
Het |
| Or10a3n |
A |
G |
7: 108,493,309 (GRCm39) |
Y107H |
probably damaging |
Het |
| Or51f1 |
A |
G |
7: 102,505,809 (GRCm39) |
Y227H |
probably damaging |
Het |
| Or51t4 |
A |
T |
7: 102,598,656 (GRCm39) |
Y328F |
probably benign |
Het |
| Or5b109 |
T |
C |
19: 13,212,259 (GRCm39) |
I215T |
probably damaging |
Het |
| P2rx1 |
A |
G |
11: 72,900,026 (GRCm39) |
N148D |
probably benign |
Het |
| Pogz |
T |
A |
3: 94,787,107 (GRCm39) |
S1232T |
probably damaging |
Het |
| Polr3b |
C |
A |
10: 84,520,049 (GRCm39) |
T655N |
probably damaging |
Het |
| Prss34 |
T |
C |
17: 25,517,882 (GRCm39) |
|
probably null |
Het |
| Rhpn2 |
A |
G |
7: 35,090,178 (GRCm39) |
|
probably null |
Het |
| Runx1 |
T |
A |
16: 92,410,648 (GRCm39) |
D256V |
probably damaging |
Het |
| Shc1 |
C |
A |
3: 89,334,715 (GRCm39) |
Q525K |
probably benign |
Het |
| Slc10a5 |
T |
C |
3: 10,400,507 (GRCm39) |
D51G |
probably benign |
Het |
| Slc6a3 |
A |
T |
13: 73,719,642 (GRCm39) |
N557I |
probably benign |
Het |
| Slmap |
C |
T |
14: 26,254,586 (GRCm39) |
R32H |
probably damaging |
Het |
| Spata31d1c |
T |
C |
13: 65,183,985 (GRCm39) |
I509T |
probably benign |
Het |
| Spata31e4 |
A |
T |
13: 50,855,007 (GRCm39) |
E215V |
probably damaging |
Het |
| Srr |
C |
A |
11: 74,801,134 (GRCm39) |
V138F |
probably benign |
Het |
| Tas2r118 |
G |
A |
6: 23,969,785 (GRCm39) |
T92I |
possibly damaging |
Het |
| Tcaf2 |
A |
T |
6: 42,601,300 (GRCm39) |
*920K |
probably null |
Het |
| Tenm2 |
T |
A |
11: 35,954,729 (GRCm39) |
Y1141F |
probably damaging |
Het |
| Thoc6 |
T |
C |
17: 23,887,841 (GRCm39) |
N322S |
probably benign |
Het |
| Tlcd2 |
A |
G |
11: 75,359,417 (GRCm39) |
I70V |
probably benign |
Het |
| Tmem214 |
A |
G |
5: 31,028,795 (GRCm39) |
D128G |
possibly damaging |
Het |
| Trav13d-4 |
T |
C |
14: 53,995,238 (GRCm39) |
V64A |
probably benign |
Het |
| Tyro3 |
T |
C |
2: 119,632,845 (GRCm39) |
W122R |
probably damaging |
Het |
| Ugcg |
A |
G |
4: 59,213,246 (GRCm39) |
D144G |
possibly damaging |
Het |
| Uimc1 |
T |
C |
13: 55,178,828 (GRCm39) |
D627G |
probably benign |
Het |
| Utp6 |
T |
C |
11: 79,853,099 (GRCm39) |
I13V |
probably benign |
Het |
| Vmn2r99 |
A |
G |
17: 19,614,605 (GRCm39) |
K775R |
probably damaging |
Het |
| Wdfy3 |
CG |
C |
5: 102,030,827 (GRCm39) |
|
probably null |
Het |
| Zw10 |
C |
T |
9: 48,982,944 (GRCm39) |
T525I |
probably benign |
Het |
|
| Other mutations in Kdm3b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00162:Kdm3b
|
APN |
18 |
34,942,462 (GRCm39) |
missense |
probably benign |
0.03 |
|
IGL01357:Kdm3b
|
APN |
18 |
34,926,067 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01615:Kdm3b
|
APN |
18 |
34,962,284 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01980:Kdm3b
|
APN |
18 |
34,967,289 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02277:Kdm3b
|
APN |
18 |
34,956,717 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02346:Kdm3b
|
APN |
18 |
34,967,291 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02417:Kdm3b
|
APN |
18 |
34,941,630 (GRCm39) |
missense |
probably benign |
0.03 |
|
IGL02531:Kdm3b
|
APN |
18 |
34,928,782 (GRCm39) |
missense |
probably benign |
|
|
IGL02589:Kdm3b
|
APN |
18 |
34,945,471 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
IGL02793:Kdm3b
|
APN |
18 |
34,962,072 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03121:Kdm3b
|
APN |
18 |
34,928,762 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL03123:Kdm3b
|
APN |
18 |
34,942,544 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL03128:Kdm3b
|
APN |
18 |
34,960,480 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Affable
|
UTSW |
18 |
34,926,058 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Dotage
|
UTSW |
18 |
34,960,435 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Endearing
|
UTSW |
18 |
34,960,381 (GRCm39) |
splice site |
probably null |
|
|
Oldtimer
|
UTSW |
18 |
34,956,752 (GRCm39) |
nonsense |
probably null |
|
|
PIT4445001:Kdm3b
|
UTSW |
18 |
34,926,168 (GRCm39) |
nonsense |
probably null |
|
|
R0068:Kdm3b
|
UTSW |
18 |
34,957,827 (GRCm39) |
missense |
probably benign |
0.18 |
|
R0068:Kdm3b
|
UTSW |
18 |
34,957,827 (GRCm39) |
missense |
probably benign |
0.18 |
|
R0233:Kdm3b
|
UTSW |
18 |
34,942,473 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R0265:Kdm3b
|
UTSW |
18 |
34,928,716 (GRCm39) |
splice site |
probably benign |
|
|
R0306:Kdm3b
|
UTSW |
18 |
34,937,070 (GRCm39) |
missense |
probably benign |
0.35 |
|
R0941:Kdm3b
|
UTSW |
18 |
34,936,605 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0970:Kdm3b
|
UTSW |
18 |
34,942,092 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1061:Kdm3b
|
UTSW |
18 |
34,929,915 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1104:Kdm3b
|
UTSW |
18 |
34,952,864 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1221:Kdm3b
|
UTSW |
18 |
34,941,298 (GRCm39) |
missense |
possibly damaging |
0.57 |
|
R1486:Kdm3b
|
UTSW |
18 |
34,967,357 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1523:Kdm3b
|
UTSW |
18 |
34,926,226 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1558:Kdm3b
|
UTSW |
18 |
34,942,149 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1585:Kdm3b
|
UTSW |
18 |
34,942,345 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1601:Kdm3b
|
UTSW |
18 |
34,941,784 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1650:Kdm3b
|
UTSW |
18 |
34,942,168 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R1772:Kdm3b
|
UTSW |
18 |
34,936,557 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1853:Kdm3b
|
UTSW |
18 |
34,966,446 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1934:Kdm3b
|
UTSW |
18 |
34,946,597 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1959:Kdm3b
|
UTSW |
18 |
34,945,448 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
R2079:Kdm3b
|
UTSW |
18 |
34,936,570 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2102:Kdm3b
|
UTSW |
18 |
34,963,200 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2121:Kdm3b
|
UTSW |
18 |
34,929,833 (GRCm39) |
splice site |
probably benign |
|
|
R2281:Kdm3b
|
UTSW |
18 |
34,941,472 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3719:Kdm3b
|
UTSW |
18 |
34,941,724 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3755:Kdm3b
|
UTSW |
18 |
34,941,349 (GRCm39) |
missense |
probably benign |
|
|
R3857:Kdm3b
|
UTSW |
18 |
34,966,440 (GRCm39) |
missense |
probably benign |
|
|
R4165:Kdm3b
|
UTSW |
18 |
34,928,797 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4166:Kdm3b
|
UTSW |
18 |
34,928,797 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4372:Kdm3b
|
UTSW |
18 |
34,960,497 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4672:Kdm3b
|
UTSW |
18 |
34,941,630 (GRCm39) |
missense |
probably benign |
|
|
R4933:Kdm3b
|
UTSW |
18 |
34,943,446 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4969:Kdm3b
|
UTSW |
18 |
34,955,428 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5009:Kdm3b
|
UTSW |
18 |
34,957,763 (GRCm39) |
missense |
probably benign |
0.42 |
|
R5059:Kdm3b
|
UTSW |
18 |
34,910,250 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R5092:Kdm3b
|
UTSW |
18 |
34,946,515 (GRCm39) |
missense |
probably benign |
0.16 |
|
R5270:Kdm3b
|
UTSW |
18 |
34,960,467 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5816:Kdm3b
|
UTSW |
18 |
34,961,522 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5970:Kdm3b
|
UTSW |
18 |
34,962,342 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6244:Kdm3b
|
UTSW |
18 |
34,926,058 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6705:Kdm3b
|
UTSW |
18 |
34,952,926 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6723:Kdm3b
|
UTSW |
18 |
34,926,058 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6909:Kdm3b
|
UTSW |
18 |
34,960,381 (GRCm39) |
splice site |
probably null |
|
|
R6958:Kdm3b
|
UTSW |
18 |
34,941,336 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7026:Kdm3b
|
UTSW |
18 |
34,955,517 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R7289:Kdm3b
|
UTSW |
18 |
34,927,557 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7488:Kdm3b
|
UTSW |
18 |
34,957,934 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R7587:Kdm3b
|
UTSW |
18 |
34,930,080 (GRCm39) |
splice site |
probably null |
|
|
R7695:Kdm3b
|
UTSW |
18 |
34,927,612 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R7846:Kdm3b
|
UTSW |
18 |
34,942,293 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7984:Kdm3b
|
UTSW |
18 |
34,956,752 (GRCm39) |
nonsense |
probably null |
|
|
R7997:Kdm3b
|
UTSW |
18 |
34,941,336 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8035:Kdm3b
|
UTSW |
18 |
34,941,781 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8064:Kdm3b
|
UTSW |
18 |
34,946,460 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R8141:Kdm3b
|
UTSW |
18 |
34,961,599 (GRCm39) |
nonsense |
probably null |
|
|
R8302:Kdm3b
|
UTSW |
18 |
34,967,388 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8328:Kdm3b
|
UTSW |
18 |
34,926,123 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8443:Kdm3b
|
UTSW |
18 |
34,926,129 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8513:Kdm3b
|
UTSW |
18 |
34,926,129 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8515:Kdm3b
|
UTSW |
18 |
34,926,129 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8523:Kdm3b
|
UTSW |
18 |
34,926,129 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8717:Kdm3b
|
UTSW |
18 |
34,952,840 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8725:Kdm3b
|
UTSW |
18 |
34,960,435 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8727:Kdm3b
|
UTSW |
18 |
34,960,435 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8762:Kdm3b
|
UTSW |
18 |
34,937,157 (GRCm39) |
missense |
probably benign |
|
|
R8835:Kdm3b
|
UTSW |
18 |
34,941,802 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8918:Kdm3b
|
UTSW |
18 |
34,970,650 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9015:Kdm3b
|
UTSW |
18 |
34,963,212 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9144:Kdm3b
|
UTSW |
18 |
34,927,558 (GRCm39) |
missense |
probably benign |
|
|
R9246:Kdm3b
|
UTSW |
18 |
34,941,480 (GRCm39) |
nonsense |
probably null |
|
|
R9376:Kdm3b
|
UTSW |
18 |
34,970,718 (GRCm39) |
missense |
probably damaging |
0.99 |
|
X0028:Kdm3b
|
UTSW |
18 |
34,932,319 (GRCm39) |
splice site |
probably null |
|
|
X0067:Kdm3b
|
UTSW |
18 |
34,956,570 (GRCm39) |
missense |
probably benign |
0.00 |
|
Z1176:Kdm3b
|
UTSW |
18 |
34,942,122 (GRCm39) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- AGTCTCACTCCTCTGCAGAGTC -3'
(R):5'- GAATCCTGTCTGCAAGCCAAG -3'
Sequencing Primer
(F):5'- GAGTCTGCACCTTTAGCAAAG -3'
(R):5'- TGTCTGCAAGCCAAGCTTCG -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation