Incidental Mutation 'R4804:Kdm1b'
| ID |
370570 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1b
|
| Ensembl Gene |
ENSMUSG00000038080 |
| Gene Name |
lysine (K)-specific demethylase 1B |
| Synonyms |
Aof1, 4632428N09Rik |
| MMRRC Submission |
041998-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.406)
|
| Stock # |
R4804 (G1)
|
| Quality Score |
211 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
47196849-47238085 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 47216553 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Tryptophan
at position 308
(R308W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000038373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000037025]
|
| AlphaFold |
Q8CIG3 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000037025
AA Change: R308W
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: R308W
| 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 |
noncoding transcript
Transcript: ENSMUST00000128977
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131120
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000143518
AA Change: R24W
|
| SMART Domains |
Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: R24W
| 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 |
0.6467 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.9%
- 20x: 94.2%
|
| Validation Efficiency |
99% (78/79) |
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930527J03Rik |
T |
C |
1: 178,103,675 (GRCm39) |
|
noncoding transcript |
Het |
| Ap4e1 |
T |
C |
2: 126,885,678 (GRCm39) |
|
probably null |
Het |
| Apbb1ip |
T |
C |
2: 22,713,610 (GRCm39) |
|
probably null |
Het |
| Apol11b |
T |
A |
15: 77,519,466 (GRCm39) |
I205F |
probably damaging |
Het |
| Arl6ip1 |
A |
T |
7: 117,728,775 (GRCm39) |
|
probably null |
Het |
| Barx2 |
A |
G |
9: 31,758,108 (GRCm39) |
S277P |
unknown |
Het |
| BC035947 |
T |
G |
1: 78,474,513 (GRCm39) |
D673A |
probably damaging |
Het |
| Cacna2d1 |
A |
T |
5: 16,564,206 (GRCm39) |
I930F |
probably damaging |
Het |
| Cd226 |
T |
C |
18: 89,225,292 (GRCm39) |
V63A |
possibly damaging |
Het |
| Cdk8 |
A |
G |
5: 146,233,209 (GRCm39) |
K236E |
probably damaging |
Het |
| Cds1 |
T |
C |
5: 101,969,389 (GRCm39) |
L449P |
probably damaging |
Het |
| Celsr1 |
T |
C |
15: 85,822,154 (GRCm39) |
D1721G |
possibly damaging |
Het |
| Chtf18 |
T |
C |
17: 25,938,231 (GRCm39) |
D934G |
probably benign |
Het |
| Clk4 |
T |
A |
11: 51,172,150 (GRCm39) |
L271Q |
probably damaging |
Het |
| Cnnm1 |
C |
A |
19: 43,480,014 (GRCm39) |
T853N |
probably benign |
Het |
| Col26a1 |
A |
G |
5: 136,865,579 (GRCm39) |
V103A |
probably damaging |
Het |
| D5Ertd579e |
C |
T |
5: 36,786,996 (GRCm39) |
|
probably null |
Het |
| Ddx39a |
A |
G |
8: 84,447,724 (GRCm39) |
K190E |
probably damaging |
Het |
| Dgkg |
G |
A |
16: 22,393,943 (GRCm39) |
|
probably benign |
Het |
| Dnajc14 |
A |
T |
10: 128,649,926 (GRCm39) |
H477L |
probably benign |
Het |
| Dytn |
A |
G |
1: 63,682,525 (GRCm39) |
V374A |
probably benign |
Het |
| Gfra2 |
T |
C |
14: 71,163,361 (GRCm39) |
Y215H |
possibly damaging |
Het |
| Grik1 |
A |
G |
16: 87,754,457 (GRCm39) |
I376T |
probably damaging |
Het |
| Gzmm |
A |
T |
10: 79,530,890 (GRCm39) |
T231S |
probably benign |
Het |
| Hecw1 |
A |
G |
13: 14,480,570 (GRCm39) |
S499P |
probably benign |
Het |
| Hhla1 |
T |
C |
15: 65,794,948 (GRCm39) |
I511V |
probably benign |
Het |
| Ifnlr1 |
A |
G |
4: 135,432,647 (GRCm39) |
D361G |
possibly damaging |
Het |
| Ikzf3 |
A |
G |
11: 98,381,400 (GRCm39) |
V60A |
probably benign |
Het |
| Ipo4 |
G |
C |
14: 55,868,313 (GRCm39) |
R495G |
possibly damaging |
Het |
| Kat2b-ps |
A |
T |
5: 93,540,392 (GRCm39) |
|
noncoding transcript |
Het |
| Mblac2 |
T |
A |
13: 81,898,428 (GRCm39) |
L268* |
probably null |
Het |
| Mipep |
C |
T |
14: 61,040,401 (GRCm39) |
T307I |
probably damaging |
Het |
| Ms4a14 |
A |
G |
19: 11,281,404 (GRCm39) |
S385P |
possibly damaging |
Het |
| Myh2 |
T |
A |
11: 67,077,328 (GRCm39) |
I821N |
possibly damaging |
Het |
| Myo5c |
A |
T |
9: 75,152,306 (GRCm39) |
I65F |
probably damaging |
Het |
| Neurog1 |
A |
G |
13: 56,399,579 (GRCm39) |
L56P |
probably benign |
Het |
| Nrsn1 |
C |
A |
13: 25,437,580 (GRCm39) |
C116F |
probably benign |
Het |
| Nscme3l |
A |
T |
19: 5,553,028 (GRCm39) |
M251K |
possibly damaging |
Het |
| Nynrin |
T |
C |
14: 56,102,326 (GRCm39) |
V665A |
probably benign |
Het |
| Or10w1 |
A |
G |
19: 13,631,882 (GRCm39) |
M30V |
probably benign |
Het |
| Or2w1b |
T |
A |
13: 21,300,175 (GRCm39) |
Y104* |
probably null |
Het |
| Or5ak20 |
T |
C |
2: 85,183,425 (GRCm39) |
I282V |
probably benign |
Het |
| Pakap |
T |
C |
4: 57,854,688 (GRCm39) |
S67P |
probably benign |
Het |
| Pcdhac1 |
C |
T |
18: 37,224,231 (GRCm39) |
S348L |
possibly damaging |
Het |
| Pcnx4 |
T |
C |
12: 72,620,976 (GRCm39) |
I932T |
probably benign |
Het |
| Pfkl |
G |
A |
10: 77,827,228 (GRCm39) |
T486I |
probably benign |
Het |
| Pi4ka |
A |
T |
16: 17,126,025 (GRCm39) |
M1115K |
possibly damaging |
Het |
| Rilpl1 |
A |
G |
5: 124,631,828 (GRCm39) |
W173R |
probably damaging |
Het |
| Rnf111 |
A |
T |
9: 70,338,239 (GRCm39) |
C900S |
possibly damaging |
Het |
| Ryr2 |
A |
G |
13: 11,731,983 (GRCm39) |
V2319A |
probably damaging |
Het |
| Scnn1g |
AATCCTGCAGGTGA |
AA |
7: 121,362,303 (GRCm39) |
|
probably null |
Het |
| Slc25a13 |
A |
T |
6: 6,109,213 (GRCm39) |
L383H |
probably damaging |
Het |
| Slco2a1 |
C |
T |
9: 102,950,383 (GRCm39) |
P325L |
probably damaging |
Het |
| Stoml2 |
T |
C |
4: 43,029,882 (GRCm39) |
N162S |
probably benign |
Het |
| Syne1 |
G |
T |
10: 5,299,310 (GRCm39) |
Q982K |
possibly damaging |
Het |
| Tbc1d31 |
C |
T |
15: 57,814,502 (GRCm39) |
Q568* |
probably null |
Het |
| Tbc1d9 |
G |
A |
8: 83,982,554 (GRCm39) |
|
probably null |
Het |
| Tbx3 |
A |
G |
5: 119,818,577 (GRCm39) |
D384G |
possibly damaging |
Het |
| Tecta |
T |
C |
9: 42,309,533 (GRCm39) |
I14V |
probably benign |
Het |
| Tgm1 |
A |
T |
14: 55,943,076 (GRCm39) |
V588E |
probably benign |
Het |
| Tpk1 |
A |
C |
6: 43,570,012 (GRCm39) |
|
probably benign |
Het |
| Tspear |
A |
T |
10: 77,612,791 (GRCm39) |
|
probably null |
Het |
| Ubxn10 |
G |
T |
4: 138,448,515 (GRCm39) |
Q54K |
possibly damaging |
Het |
| Ubxn4 |
C |
T |
1: 128,194,141 (GRCm39) |
R312* |
probably null |
Het |
| Vmn1r230 |
A |
T |
17: 21,067,345 (GRCm39) |
K178M |
probably damaging |
Het |
| Zfp143 |
G |
A |
7: 109,687,976 (GRCm39) |
V445I |
probably damaging |
Het |
| Zfp688 |
C |
A |
7: 127,021,057 (GRCm39) |
W40C |
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 |
|
|
R0599:Kdm1b
|
UTSW |
13 |
47,212,286 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
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 |
|
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'- CTGGCTGTTTTGCAAGTCCC -3'
(R):5'- TGGCTGACGACTCTGCTAGTTAG -3'
Sequencing Primer
(F):5'- CAAGTCCCAGCTTGCAGAG -3'
(R):5'- AGTTAGTCACCATGGCTGAC -3'
|
| Posted On |
2016-02-04 |
Incidental Mutation