Incidental Mutation 'R3897:Kdm4b'
| ID |
309028 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4b
|
| Ensembl Gene |
ENSMUSG00000024201 |
| Gene Name |
lysine (K)-specific demethylase 4B |
| Synonyms |
Jmjd2b, 4732474L06Rik |
| MMRRC Submission |
040808-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R3897 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
56633062-56709870 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 56703955 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Arginine
at position 233
(C233R)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025036]
[ENSMUST00000086835]
|
| AlphaFold |
Q91VY5 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000025036
AA Change: C776R
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000025036
Gene: ENSMUSG00000024201
AA Change: C776R
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
14 |
56 |
5.88e-17 |
SMART |
|
low complexity region
|
61 |
68 |
N/A |
INTRINSIC |
|
JmjC
|
143 |
309 |
1.19e-59 |
SMART |
|
low complexity region
|
349 |
361 |
N/A |
INTRINSIC |
|
low complexity region
|
380 |
399 |
N/A |
INTRINSIC |
|
low complexity region
|
443 |
449 |
N/A |
INTRINSIC |
|
low complexity region
|
481 |
495 |
N/A |
INTRINSIC |
|
low complexity region
|
511 |
537 |
N/A |
INTRINSIC |
|
PHD
|
719 |
777 |
2.5e-5 |
SMART |
|
PHD
|
839 |
895 |
7.07e-5 |
SMART |
|
TUDOR
|
905 |
962 |
1.68e-9 |
SMART |
|
TUDOR
|
963 |
1019 |
7.94e-11 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000086835
AA Change: C769R
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000084045
Gene: ENSMUSG00000024201
AA Change: C769R
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
14 |
56 |
5.88e-17 |
SMART |
|
low complexity region
|
61 |
68 |
N/A |
INTRINSIC |
|
JmjC
|
143 |
309 |
1.19e-59 |
SMART |
|
low complexity region
|
349 |
361 |
N/A |
INTRINSIC |
|
low complexity region
|
380 |
399 |
N/A |
INTRINSIC |
|
low complexity region
|
443 |
449 |
N/A |
INTRINSIC |
|
low complexity region
|
481 |
495 |
N/A |
INTRINSIC |
|
low complexity region
|
511 |
537 |
N/A |
INTRINSIC |
|
PHD
|
712 |
770 |
2.5e-5 |
SMART |
|
PHD
|
832 |
888 |
7.07e-5 |
SMART |
|
TUDOR
|
898 |
954 |
2.31e-12 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000141507
AA Change: C233R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000116789
Gene: ENSMUSG00000024201
AA Change: C233R
| Domain | Start | End | E-Value | Type |
|---|
|
PHD
|
177 |
235 |
2.5e-5 |
SMART |
|
PHD
|
297 |
353 |
7.07e-5 |
SMART |
|
TUDOR
|
363 |
420 |
1.68e-9 |
SMART |
|
TUDOR
|
421 |
477 |
7.94e-11 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147489
|
| Meta Mutation Damage Score |
0.9729 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.4%
|
| Validation Efficiency |
97% (35/36) |
| MGI Phenotype |
PHENOTYPE: Mice homozygous for a targeted allele lacking demethylase activity exhibit no gross abnormalities. Mice homozygous for a conditional allele activated in mammary gland epithelial cells exhibit delayed mammary gland development with reduced branching. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 32 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam15 |
T |
C |
3: 89,254,245 (GRCm39) |
H184R |
probably benign |
Het |
| Ap1g1 |
A |
G |
8: 110,581,631 (GRCm39) |
D633G |
probably damaging |
Het |
| Arhgef28 |
C |
T |
13: 98,093,084 (GRCm39) |
R999H |
probably damaging |
Het |
| Armc3 |
T |
C |
2: 19,273,988 (GRCm39) |
S341P |
probably damaging |
Het |
| Cmya5 |
T |
C |
13: 93,233,189 (GRCm39) |
E633G |
possibly damaging |
Het |
| Colgalt1 |
G |
A |
8: 72,072,306 (GRCm39) |
M275I |
probably damaging |
Het |
| Commd7 |
T |
C |
2: 153,464,710 (GRCm39) |
T23A |
probably benign |
Het |
| Cts3 |
A |
G |
13: 61,712,800 (GRCm39) |
Y307H |
probably benign |
Het |
| Dlgap4 |
C |
A |
2: 156,587,989 (GRCm39) |
P89Q |
probably damaging |
Het |
| Ecm1 |
A |
G |
3: 95,643,298 (GRCm39) |
L334P |
probably damaging |
Het |
| Fzd8 |
G |
A |
18: 9,214,939 (GRCm39) |
V674I |
possibly damaging |
Het |
| Gosr2 |
A |
G |
11: 103,588,472 (GRCm39) |
Y5H |
possibly damaging |
Het |
| Gria4 |
T |
A |
9: 4,513,260 (GRCm39) |
D283V |
probably damaging |
Het |
| Hivep2 |
C |
A |
10: 14,004,713 (GRCm39) |
T437K |
probably benign |
Het |
| Iqcm |
C |
T |
8: 76,480,028 (GRCm39) |
R329C |
probably damaging |
Het |
| Ltbp1 |
T |
C |
17: 75,581,011 (GRCm39) |
C391R |
probably damaging |
Het |
| Man2b1 |
G |
T |
8: 85,823,577 (GRCm39) |
|
probably benign |
Het |
| Mgat4f |
A |
G |
1: 134,318,176 (GRCm39) |
D316G |
possibly damaging |
Het |
| Nisch |
A |
G |
14: 30,912,957 (GRCm39) |
|
probably benign |
Het |
| Nrxn2 |
T |
G |
19: 6,569,287 (GRCm39) |
D1394E |
probably damaging |
Het |
| Or4c12 |
T |
C |
2: 89,774,153 (GRCm39) |
E102G |
probably benign |
Het |
| Or4k77 |
T |
C |
2: 111,199,106 (GRCm39) |
L43P |
possibly damaging |
Het |
| Pabpc6 |
T |
C |
17: 9,888,056 (GRCm39) |
D165G |
probably benign |
Het |
| Psat1 |
A |
G |
19: 15,896,817 (GRCm39) |
|
probably null |
Het |
| Psd |
A |
C |
19: 46,313,024 (GRCm39) |
N115K |
possibly damaging |
Het |
| Rfwd3 |
C |
T |
8: 112,014,874 (GRCm39) |
R326Q |
probably damaging |
Het |
| Rnf144a |
A |
G |
12: 26,360,712 (GRCm39) |
V275A |
probably damaging |
Het |
| Slc35b3 |
A |
G |
13: 39,118,739 (GRCm39) |
F356L |
probably benign |
Het |
| Tmc4 |
A |
G |
7: 3,674,087 (GRCm39) |
V364A |
probably benign |
Het |
| Tmem203 |
T |
C |
2: 25,145,935 (GRCm39) |
F85S |
probably benign |
Het |
| Tra2a |
T |
C |
6: 49,222,476 (GRCm39) |
|
probably benign |
Het |
| Ttc21b |
C |
T |
2: 66,065,413 (GRCm39) |
E454K |
probably benign |
Het |
|
| Other mutations in Kdm4b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01293:Kdm4b
|
APN |
17 |
56,660,019 (GRCm39) |
missense |
probably benign |
0.28 |
|
IGL01408:Kdm4b
|
APN |
17 |
56,660,518 (GRCm39) |
splice site |
probably benign |
|
|
IGL01610:Kdm4b
|
APN |
17 |
56,660,522 (GRCm39) |
splice site |
probably benign |
|
|
IGL01936:Kdm4b
|
APN |
17 |
56,704,355 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01964:Kdm4b
|
APN |
17 |
56,696,256 (GRCm39) |
splice site |
probably null |
|
|
IGL02151:Kdm4b
|
APN |
17 |
56,703,234 (GRCm39) |
missense |
probably benign |
0.05 |
|
IGL02596:Kdm4b
|
APN |
17 |
56,706,706 (GRCm39) |
missense |
probably benign |
0.14 |
|
IGL02975:Kdm4b
|
APN |
17 |
56,682,996 (GRCm39) |
splice site |
probably null |
|
|
IGL03172:Kdm4b
|
APN |
17 |
56,708,649 (GRCm39) |
missense |
probably damaging |
0.98 |
|
Coelestinum
|
UTSW |
17 |
56,660,091 (GRCm39) |
missense |
probably benign |
0.31 |
|
mistflower
|
UTSW |
17 |
56,696,564 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R0193:Kdm4b
|
UTSW |
17 |
56,700,952 (GRCm39) |
missense |
probably benign |
0.04 |
|
R0311:Kdm4b
|
UTSW |
17 |
56,693,200 (GRCm39) |
missense |
probably benign |
0.42 |
|
R0331:Kdm4b
|
UTSW |
17 |
56,693,289 (GRCm39) |
splice site |
probably benign |
|
|
R1109:Kdm4b
|
UTSW |
17 |
56,706,430 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1499:Kdm4b
|
UTSW |
17 |
56,707,025 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1895:Kdm4b
|
UTSW |
17 |
56,704,340 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1985:Kdm4b
|
UTSW |
17 |
56,708,302 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2087:Kdm4b
|
UTSW |
17 |
56,696,564 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R2185:Kdm4b
|
UTSW |
17 |
56,700,750 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2904:Kdm4b
|
UTSW |
17 |
56,662,884 (GRCm39) |
missense |
probably benign |
0.03 |
|
R3792:Kdm4b
|
UTSW |
17 |
56,662,944 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4661:Kdm4b
|
UTSW |
17 |
56,706,459 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4685:Kdm4b
|
UTSW |
17 |
56,708,675 (GRCm39) |
missense |
probably benign |
0.06 |
|
R4716:Kdm4b
|
UTSW |
17 |
56,693,178 (GRCm39) |
missense |
probably benign |
0.10 |
|
R4790:Kdm4b
|
UTSW |
17 |
56,708,618 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R4864:Kdm4b
|
UTSW |
17 |
56,660,091 (GRCm39) |
missense |
probably benign |
0.31 |
|
R5700:Kdm4b
|
UTSW |
17 |
56,658,700 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R5963:Kdm4b
|
UTSW |
17 |
56,706,732 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6003:Kdm4b
|
UTSW |
17 |
56,703,916 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6029:Kdm4b
|
UTSW |
17 |
56,703,576 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6769:Kdm4b
|
UTSW |
17 |
56,658,754 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R6771:Kdm4b
|
UTSW |
17 |
56,658,754 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R6927:Kdm4b
|
UTSW |
17 |
56,706,435 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7041:Kdm4b
|
UTSW |
17 |
56,703,592 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7230:Kdm4b
|
UTSW |
17 |
56,676,155 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7275:Kdm4b
|
UTSW |
17 |
56,703,333 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7454:Kdm4b
|
UTSW |
17 |
56,696,639 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7455:Kdm4b
|
UTSW |
17 |
56,703,657 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7457:Kdm4b
|
UTSW |
17 |
56,703,319 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8171:Kdm4b
|
UTSW |
17 |
56,696,534 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8367:Kdm4b
|
UTSW |
17 |
56,662,875 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8524:Kdm4b
|
UTSW |
17 |
56,706,384 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8810:Kdm4b
|
UTSW |
17 |
56,706,771 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9260:Kdm4b
|
UTSW |
17 |
56,701,775 (GRCm39) |
missense |
probably benign |
|
|
R9459:Kdm4b
|
UTSW |
17 |
56,706,509 (GRCm39) |
missense |
probably benign |
0.15 |
|
R9466:Kdm4b
|
UTSW |
17 |
56,696,548 (GRCm39) |
missense |
probably benign |
0.04 |
|
R9559:Kdm4b
|
UTSW |
17 |
56,693,228 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0024:Kdm4b
|
UTSW |
17 |
56,708,278 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCAGTGTGAAGGGCTCTAGG -3'
(R):5'- AACAGCATTCCTGAGGGACAG -3'
Sequencing Primer
(F):5'- GACACTGTCCAGGGTTCTG -3'
(R):5'- ACAGATCAGTGTGGTGAGGTGC -3'
|
| Posted On |
2015-04-17 |
Incidental Mutation