Incidental Mutation 'R0599:Kdm1b'
ID |
55248 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm1b
|
Ensembl Gene |
ENSMUSG00000038080 |
Gene Name |
lysine (K)-specific demethylase 1B |
Synonyms |
Aof1, 4632428N09Rik |
MMRRC Submission |
038788-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.504)
|
Stock # |
R0599 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
13 |
Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 47212286 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Valine
at position 190
(D190V)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
AlphaFold |
Q8CIG3 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000037025
AA Change: D190V
PolyPhen 2
Score 0.469 (Sensitivity: 0.89; Specificity: 0.90)
|
SMART Domains |
Protein: ENSMUSP00000038373 Gene: ENSMUSG00000038080 AA Change: D190V
Domain | Start | End | E-Value | Type |
Pfam:zf-CW
|
138 |
191 |
2.6e-13 |
PFAM |
low complexity region
|
235 |
253 |
N/A |
INTRINSIC |
Pfam:SWIRM
|
286 |
369 |
6e-12 |
PFAM |
Pfam:Pyr_redox_2
|
368 |
490 |
3.1e-8 |
PFAM |
Pfam:Thi4
|
375 |
446 |
2.2e-10 |
PFAM |
Pfam:FAD_binding_3
|
388 |
423 |
4.1e-7 |
PFAM |
Pfam:HI0933_like
|
389 |
428 |
1.6e-7 |
PFAM |
Pfam:FAD_binding_2
|
390 |
428 |
1.6e-6 |
PFAM |
Pfam:Pyr_redox
|
390 |
438 |
8e-8 |
PFAM |
Pfam:NAD_binding_8
|
393 |
460 |
1.6e-13 |
PFAM |
Pfam:Amino_oxidase
|
398 |
824 |
3.7e-86 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000143518
|
SMART Domains |
Protein: ENSMUSP00000114999 Gene: ENSMUSG00000038080
Domain | Start | End | E-Value | Type |
Pfam:SWIRM
|
3 |
86 |
1.1e-12 |
PFAM |
Pfam:Thi4
|
91 |
163 |
3.5e-10 |
PFAM |
Pfam:FAD_binding_3
|
105 |
140 |
3.5e-7 |
PFAM |
Pfam:HI0933_like
|
106 |
145 |
1.7e-7 |
PFAM |
Pfam:Pyr_redox_2
|
106 |
251 |
1.5e-10 |
PFAM |
Pfam:FAD_binding_2
|
107 |
150 |
5.7e-7 |
PFAM |
Pfam:Pyr_redox
|
107 |
158 |
6.4e-8 |
PFAM |
Pfam:Pyr_redox_3
|
109 |
288 |
1.2e-13 |
PFAM |
Pfam:NAD_binding_8
|
110 |
177 |
2.3e-13 |
PFAM |
Pfam:Amino_oxidase
|
115 |
181 |
8.6e-19 |
PFAM |
Pfam:Amino_oxidase
|
178 |
441 |
4.5e-63 |
PFAM |
|
Meta Mutation Damage Score |
0.3057 |
Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.9%
- 10x: 97.5%
- 20x: 95.0%
|
Validation Efficiency |
98% (80/82) |
MGI Phenotype |
PHENOTYPE: Homozygous null mice of both sexes are viable, grossly normal and male mice are fertile; however, heterozygous progeny of homozygous null mothers display severe placental defects, embryonic growth impairment, neural tube defects and pericardial edema, and do not survive past E10.5. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 78 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A2ml1 |
A |
G |
6: 128,529,208 (GRCm39) |
L978P |
probably damaging |
Het |
Abcb1a |
C |
T |
5: 8,748,539 (GRCm39) |
T290M |
probably benign |
Het |
Abcd3 |
A |
T |
3: 121,558,742 (GRCm39) |
F585I |
probably damaging |
Het |
Abtb3 |
G |
A |
10: 85,494,200 (GRCm39) |
G1106D |
probably damaging |
Het |
Acan |
A |
G |
7: 78,761,038 (GRCm39) |
|
probably benign |
Het |
Anxa6 |
T |
C |
11: 54,870,292 (GRCm39) |
D667G |
possibly damaging |
Het |
Ap3m2 |
G |
T |
8: 23,283,128 (GRCm39) |
A208D |
possibly damaging |
Het |
Arhgap17 |
A |
T |
7: 122,903,013 (GRCm39) |
|
probably benign |
Het |
Bptf |
A |
G |
11: 106,959,208 (GRCm39) |
V1838A |
probably damaging |
Het |
Brip1 |
T |
A |
11: 86,043,563 (GRCm39) |
M334L |
probably benign |
Het |
Btbd10 |
C |
T |
7: 112,934,516 (GRCm39) |
|
probably benign |
Het |
Cdh20 |
C |
A |
1: 109,980,696 (GRCm39) |
T208K |
probably damaging |
Het |
Cnga4 |
A |
G |
7: 105,055,025 (GRCm39) |
Y100C |
probably damaging |
Het |
Dnah10 |
G |
A |
5: 124,878,017 (GRCm39) |
V2644M |
probably damaging |
Het |
Dnah9 |
T |
C |
11: 65,856,515 (GRCm39) |
D2882G |
probably damaging |
Het |
Eapp |
T |
A |
12: 54,732,747 (GRCm39) |
K117M |
probably damaging |
Het |
Eml3 |
T |
C |
19: 8,916,427 (GRCm39) |
V673A |
probably benign |
Het |
Ephb4 |
G |
A |
5: 137,368,117 (GRCm39) |
C754Y |
probably damaging |
Het |
Eps8l1 |
A |
G |
7: 4,480,956 (GRCm39) |
D33G |
possibly damaging |
Het |
Farsa |
A |
G |
8: 85,594,212 (GRCm39) |
K321E |
probably damaging |
Het |
Fry |
G |
A |
5: 150,360,624 (GRCm39) |
R2090Q |
probably damaging |
Het |
Gm10283 |
A |
G |
8: 60,954,258 (GRCm39) |
|
probably benign |
Het |
Grm4 |
A |
G |
17: 27,650,464 (GRCm39) |
I844T |
probably benign |
Het |
Gtf2h3 |
A |
G |
5: 124,726,691 (GRCm39) |
D124G |
probably benign |
Het |
Gulo |
A |
T |
14: 66,227,890 (GRCm39) |
D347E |
probably damaging |
Het |
Hmcn1 |
A |
G |
1: 150,485,552 (GRCm39) |
F4350S |
possibly damaging |
Het |
Hspg2 |
A |
G |
4: 137,239,712 (GRCm39) |
D473G |
probably damaging |
Het |
Il17ra |
T |
A |
6: 120,458,466 (GRCm39) |
I539N |
probably damaging |
Het |
Insrr |
A |
G |
3: 87,720,440 (GRCm39) |
E1026G |
probably damaging |
Het |
Itga2 |
A |
T |
13: 114,993,186 (GRCm39) |
|
probably benign |
Het |
Lima1 |
A |
T |
15: 99,700,040 (GRCm39) |
N146K |
probably damaging |
Het |
Mnt |
G |
T |
11: 74,733,122 (GRCm39) |
V85L |
probably benign |
Het |
Mon2 |
T |
A |
10: 122,861,970 (GRCm39) |
|
probably benign |
Het |
Mtf1 |
T |
C |
4: 124,713,994 (GRCm39) |
|
probably benign |
Het |
Mylk4 |
T |
C |
13: 32,896,737 (GRCm39) |
|
probably null |
Het |
Myo18b |
A |
C |
5: 113,013,616 (GRCm39) |
L780R |
probably damaging |
Het |
Myo1e |
A |
G |
9: 70,283,942 (GRCm39) |
|
probably benign |
Het |
Obscn |
A |
G |
11: 58,964,522 (GRCm39) |
S705P |
probably damaging |
Het |
Ocrl |
A |
T |
X: 47,024,963 (GRCm39) |
|
probably benign |
Het |
Or1e34 |
A |
T |
11: 73,778,730 (GRCm39) |
M156K |
probably benign |
Het |
Or4c35 |
T |
C |
2: 89,808,545 (GRCm39) |
F141S |
probably benign |
Het |
Or51k1 |
A |
T |
7: 103,661,395 (GRCm39) |
C171* |
probably null |
Het |
Or52ab4 |
A |
G |
7: 102,987,393 (GRCm39) |
N44S |
probably damaging |
Het |
Otof |
T |
A |
5: 30,528,049 (GRCm39) |
K1931N |
probably damaging |
Het |
Plcxd3 |
A |
G |
15: 4,546,349 (GRCm39) |
S118G |
probably damaging |
Het |
Plcz1 |
T |
A |
6: 139,974,268 (GRCm39) |
Q58L |
probably benign |
Het |
Proser1 |
C |
A |
3: 53,386,485 (GRCm39) |
P789Q |
probably benign |
Het |
Rassf4 |
T |
C |
6: 116,622,897 (GRCm39) |
E38G |
probably damaging |
Het |
Ros1 |
A |
T |
10: 51,999,396 (GRCm39) |
Y1164N |
probably damaging |
Het |
Rpgrip1l |
A |
G |
8: 92,031,628 (GRCm39) |
I83T |
probably damaging |
Het |
Scn9a |
T |
G |
2: 66,357,143 (GRCm39) |
K1053Q |
probably damaging |
Het |
Sgsm1 |
G |
T |
5: 113,392,894 (GRCm39) |
Q1087K |
probably damaging |
Het |
Slc16a10 |
T |
C |
10: 40,017,914 (GRCm39) |
D40G |
probably benign |
Het |
Slc27a6 |
A |
G |
18: 58,689,885 (GRCm39) |
D117G |
probably damaging |
Het |
Slc2a9 |
T |
A |
5: 38,637,487 (GRCm39) |
|
probably benign |
Het |
Slc4a1 |
A |
G |
11: 102,248,741 (GRCm39) |
|
probably benign |
Het |
Smarca1 |
T |
A |
X: 46,912,303 (GRCm39) |
Q982L |
probably benign |
Het |
Sp100 |
T |
A |
1: 85,608,831 (GRCm39) |
I320N |
possibly damaging |
Het |
Stx8 |
A |
T |
11: 68,000,188 (GRCm39) |
R209S |
probably null |
Het |
Sulf2 |
T |
C |
2: 165,925,799 (GRCm39) |
T453A |
possibly damaging |
Het |
Syne2 |
AGAGTGAG |
AGAGTGAGTGAG |
12: 76,144,734 (GRCm39) |
|
probably null |
Het |
Tenm2 |
T |
A |
11: 35,915,607 (GRCm39) |
I1976F |
possibly damaging |
Het |
Tenm3 |
G |
A |
8: 48,730,745 (GRCm39) |
S1341L |
probably damaging |
Het |
Tmem130 |
C |
T |
5: 144,674,619 (GRCm39) |
V369M |
probably damaging |
Het |
Tmem200c |
A |
G |
17: 69,147,506 (GRCm39) |
K30E |
probably damaging |
Het |
Tmem225 |
A |
G |
9: 40,061,043 (GRCm39) |
I117V |
possibly damaging |
Het |
Tmt1a3 |
A |
T |
15: 100,233,264 (GRCm39) |
N152Y |
possibly damaging |
Het |
Top2a |
A |
G |
11: 98,892,243 (GRCm39) |
I1073T |
probably damaging |
Het |
Trps1 |
A |
C |
15: 50,695,256 (GRCm39) |
Y296* |
probably null |
Het |
Tubg1 |
T |
C |
11: 101,016,162 (GRCm39) |
M377T |
probably benign |
Het |
Tut7 |
A |
G |
13: 59,957,301 (GRCm39) |
V7A |
probably damaging |
Het |
Vmn1r35 |
G |
A |
6: 66,656,497 (GRCm39) |
H58Y |
probably benign |
Het |
Vmn1r56 |
G |
A |
7: 5,199,429 (GRCm39) |
H63Y |
probably benign |
Het |
Vmn1r75 |
T |
C |
7: 11,615,189 (GRCm39) |
|
probably null |
Het |
Vnn3 |
T |
C |
10: 23,741,603 (GRCm39) |
S303P |
possibly damaging |
Het |
Wdr49 |
C |
T |
3: 75,338,383 (GRCm39) |
|
probably null |
Het |
Wdr49 |
T |
C |
3: 75,357,197 (GRCm39) |
|
probably null |
Het |
Zzef1 |
T |
C |
11: 72,804,004 (GRCm39) |
L2582P |
probably damaging |
Het |
|
Other mutations in Kdm1b |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00587:Kdm1b
|
APN |
13 |
47,222,016 (GRCm39) |
missense |
probably benign |
0.01 |
IGL00924:Kdm1b
|
APN |
13 |
47,221,956 (GRCm39) |
missense |
probably benign |
|
IGL01553:Kdm1b
|
APN |
13 |
47,234,024 (GRCm39) |
missense |
probably damaging |
0.96 |
IGL01663:Kdm1b
|
APN |
13 |
47,227,213 (GRCm39) |
missense |
probably damaging |
0.99 |
IGL02385:Kdm1b
|
APN |
13 |
47,221,982 (GRCm39) |
missense |
possibly damaging |
0.49 |
IGL02505:Kdm1b
|
APN |
13 |
47,214,331 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02826:Kdm1b
|
APN |
13 |
47,233,943 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03257:Kdm1b
|
APN |
13 |
47,202,742 (GRCm39) |
missense |
probably damaging |
1.00 |
R0052:Kdm1b
|
UTSW |
13 |
47,217,593 (GRCm39) |
missense |
probably damaging |
1.00 |
R0319:Kdm1b
|
UTSW |
13 |
47,207,195 (GRCm39) |
missense |
probably benign |
|
R0426:Kdm1b
|
UTSW |
13 |
47,217,720 (GRCm39) |
splice site |
probably benign |
|
R0764:Kdm1b
|
UTSW |
13 |
47,222,079 (GRCm39) |
missense |
possibly damaging |
0.70 |
R1163:Kdm1b
|
UTSW |
13 |
47,225,398 (GRCm39) |
missense |
probably benign |
0.02 |
R1543:Kdm1b
|
UTSW |
13 |
47,221,997 (GRCm39) |
missense |
probably damaging |
0.99 |
R1584:Kdm1b
|
UTSW |
13 |
47,217,530 (GRCm39) |
missense |
probably damaging |
1.00 |
R1627:Kdm1b
|
UTSW |
13 |
47,217,707 (GRCm39) |
critical splice donor site |
probably null |
|
R1669:Kdm1b
|
UTSW |
13 |
47,222,024 (GRCm39) |
missense |
probably damaging |
1.00 |
R1758:Kdm1b
|
UTSW |
13 |
47,214,244 (GRCm39) |
missense |
probably benign |
0.00 |
R1860:Kdm1b
|
UTSW |
13 |
47,202,666 (GRCm39) |
missense |
probably benign |
0.03 |
R1907:Kdm1b
|
UTSW |
13 |
47,217,596 (GRCm39) |
missense |
probably benign |
0.00 |
R2225:Kdm1b
|
UTSW |
13 |
47,217,564 (GRCm39) |
frame shift |
probably null |
|
R2239:Kdm1b
|
UTSW |
13 |
47,227,231 (GRCm39) |
missense |
probably damaging |
1.00 |
R2271:Kdm1b
|
UTSW |
13 |
47,217,564 (GRCm39) |
frame shift |
probably null |
|
R2302:Kdm1b
|
UTSW |
13 |
47,217,564 (GRCm39) |
frame shift |
probably null |
|
R2303:Kdm1b
|
UTSW |
13 |
47,217,564 (GRCm39) |
frame shift |
probably null |
|
R2380:Kdm1b
|
UTSW |
13 |
47,227,231 (GRCm39) |
missense |
probably damaging |
1.00 |
R2442:Kdm1b
|
UTSW |
13 |
47,216,451 (GRCm39) |
missense |
probably benign |
0.32 |
R3022:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R3054:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R3545:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R3546:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R3548:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R4094:Kdm1b
|
UTSW |
13 |
47,216,496 (GRCm39) |
missense |
probably damaging |
1.00 |
R4419:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R4420:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R4502:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R4547:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R4548:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R4785:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R4793:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R4804:Kdm1b
|
UTSW |
13 |
47,216,553 (GRCm39) |
missense |
probably damaging |
1.00 |
R4882:Kdm1b
|
UTSW |
13 |
47,214,369 (GRCm39) |
missense |
probably benign |
|
R4906:Kdm1b
|
UTSW |
13 |
47,216,620 (GRCm39) |
critical splice donor site |
probably null |
|
R4965:Kdm1b
|
UTSW |
13 |
47,227,843 (GRCm39) |
missense |
probably damaging |
0.98 |
R5039:Kdm1b
|
UTSW |
13 |
47,230,962 (GRCm39) |
missense |
probably damaging |
1.00 |
R5098:Kdm1b
|
UTSW |
13 |
47,216,467 (GRCm39) |
missense |
probably damaging |
1.00 |
R5265:Kdm1b
|
UTSW |
13 |
47,216,445 (GRCm39) |
missense |
probably benign |
0.35 |
R5541:Kdm1b
|
UTSW |
13 |
47,232,672 (GRCm39) |
missense |
probably damaging |
1.00 |
R5814:Kdm1b
|
UTSW |
13 |
47,216,622 (GRCm39) |
splice site |
probably null |
|
R6046:Kdm1b
|
UTSW |
13 |
47,232,729 (GRCm39) |
missense |
possibly damaging |
0.92 |
R6798:Kdm1b
|
UTSW |
13 |
47,222,012 (GRCm39) |
missense |
probably benign |
0.00 |
R6903:Kdm1b
|
UTSW |
13 |
47,227,880 (GRCm39) |
missense |
probably benign |
0.00 |
R7831:Kdm1b
|
UTSW |
13 |
47,204,098 (GRCm39) |
missense |
probably benign |
0.17 |
R7973:Kdm1b
|
UTSW |
13 |
47,230,922 (GRCm39) |
missense |
probably benign |
0.00 |
R8181:Kdm1b
|
UTSW |
13 |
47,205,377 (GRCm39) |
critical splice donor site |
probably null |
|
R8248:Kdm1b
|
UTSW |
13 |
47,225,354 (GRCm39) |
intron |
probably benign |
|
R8821:Kdm1b
|
UTSW |
13 |
47,217,617 (GRCm39) |
missense |
possibly damaging |
0.94 |
R8831:Kdm1b
|
UTSW |
13 |
47,217,617 (GRCm39) |
missense |
possibly damaging |
0.94 |
R8842:Kdm1b
|
UTSW |
13 |
47,231,832 (GRCm39) |
missense |
probably damaging |
1.00 |
R8861:Kdm1b
|
UTSW |
13 |
47,217,582 (GRCm39) |
missense |
probably benign |
0.02 |
R8885:Kdm1b
|
UTSW |
13 |
47,207,184 (GRCm39) |
nonsense |
probably null |
|
R9038:Kdm1b
|
UTSW |
13 |
47,202,770 (GRCm39) |
missense |
probably benign |
0.07 |
R9132:Kdm1b
|
UTSW |
13 |
47,225,458 (GRCm39) |
missense |
probably benign |
0.05 |
R9268:Kdm1b
|
UTSW |
13 |
47,217,705 (GRCm39) |
missense |
probably benign |
0.00 |
R9616:Kdm1b
|
UTSW |
13 |
47,234,030 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- TGAAAGTGCCAATCTTCCCACACTC -3'
(R):5'- GGTCCTGCAACTACAGTATCACCAC -3'
Sequencing Primer
(F):5'- GCATTTTTCTTGCCAGTTAAATAGGG -3'
(R):5'- ACCATCACCATCTATGACTGTG -3'
|
Posted On |
2013-07-11 |