Incidental Mutation 'R2904:Kdm4b'
| ID |
261601 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4b
|
| Ensembl Gene |
ENSMUSG00000024201 |
| Gene Name |
lysine (K)-specific demethylase 4B |
| Synonyms |
Jmjd2b, 4732474L06Rik |
| MMRRC Submission |
040491-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2904 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
56633062-56709870 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 56662884 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glycine to Serine
at position 152
(G152S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000025036
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025036]
[ENSMUST00000086835]
[ENSMUST00000139679]
|
| AlphaFold |
Q91VY5 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000025036
AA Change: G152S
PolyPhen 2
Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000025036
Gene: ENSMUSG00000024201
AA Change: G152S
| 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 benign
Transcript: ENSMUST00000086835
AA Change: G152S
PolyPhen 2
Score 0.030 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000084045
Gene: ENSMUSG00000024201
AA Change: G152S
| 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 benign
Transcript: ENSMUST00000139679
AA Change: G152S
PolyPhen 2
Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000118089
Gene: ENSMUSG00000024201
AA Change: G152S
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
14 |
56 |
5.88e-17 |
SMART |
|
low complexity region
|
61 |
68 |
N/A |
INTRINSIC |
|
Pfam:JmjC
|
176 |
208 |
5.8e-13 |
PFAM |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.5%
|
| Validation Efficiency |
97% (30/31) |
| 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: 31 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abraxas1 |
T |
C |
5: 100,957,673 (GRCm39) |
E182G |
probably benign |
Het |
| Acot4 |
C |
G |
12: 84,090,377 (GRCm39) |
T358S |
probably benign |
Het |
| Ap2a2 |
A |
G |
7: 141,199,391 (GRCm39) |
K433E |
probably damaging |
Het |
| Card11 |
T |
A |
5: 140,874,888 (GRCm39) |
D592V |
probably benign |
Het |
| Col12a1 |
G |
T |
9: 79,559,307 (GRCm39) |
S1860R |
probably damaging |
Het |
| Crisp1 |
C |
T |
17: 40,623,895 (GRCm39) |
|
probably null |
Het |
| Dzip1l |
A |
G |
9: 99,545,722 (GRCm39) |
E657G |
probably damaging |
Het |
| Gak |
T |
C |
5: 108,772,080 (GRCm39) |
N79S |
possibly damaging |
Het |
| Gm9791 |
T |
C |
3: 34,059,336 (GRCm39) |
|
noncoding transcript |
Het |
| Gmpr2 |
T |
C |
14: 55,910,215 (GRCm39) |
V15A |
probably damaging |
Het |
| Hectd4 |
T |
C |
5: 121,430,787 (GRCm39) |
|
probably benign |
Het |
| Ift56 |
T |
C |
6: 38,378,037 (GRCm39) |
V283A |
possibly damaging |
Het |
| Kalrn |
C |
T |
16: 33,810,180 (GRCm39) |
D2525N |
possibly damaging |
Het |
| Kdm6b |
G |
A |
11: 69,296,611 (GRCm39) |
T552I |
possibly damaging |
Het |
| Kdr |
T |
C |
5: 76,127,069 (GRCm39) |
Y307C |
probably damaging |
Het |
| Kif11 |
T |
C |
19: 37,392,103 (GRCm39) |
|
probably benign |
Het |
| Kirrel1 |
C |
T |
3: 86,996,458 (GRCm39) |
M380I |
probably null |
Het |
| Madd |
C |
T |
2: 91,006,017 (GRCm39) |
V20M |
probably damaging |
Het |
| Mkrn3 |
C |
A |
7: 62,068,207 (GRCm39) |
R528L |
probably benign |
Het |
| Myom2 |
T |
C |
8: 15,148,348 (GRCm39) |
V508A |
probably benign |
Het |
| Nav1 |
T |
C |
1: 135,512,976 (GRCm39) |
D28G |
probably benign |
Het |
| Nlrp4b |
T |
A |
7: 10,448,294 (GRCm39) |
W166R |
probably damaging |
Het |
| Or14j2 |
A |
T |
17: 37,885,705 (GRCm39) |
L203Q |
possibly damaging |
Het |
| Or5p59 |
T |
C |
7: 107,702,806 (GRCm39) |
Y97H |
probably benign |
Het |
| Rassf10 |
A |
T |
7: 112,553,756 (GRCm39) |
D119V |
possibly damaging |
Het |
| Smarcc1 |
A |
G |
9: 110,003,043 (GRCm39) |
N378D |
possibly damaging |
Het |
| Tas2r118 |
A |
G |
6: 23,969,801 (GRCm39) |
F87L |
possibly damaging |
Het |
| Tasor2 |
T |
C |
13: 3,632,185 (GRCm39) |
N772S |
possibly damaging |
Het |
| Trim21 |
A |
G |
7: 102,209,178 (GRCm39) |
W282R |
probably benign |
Het |
| Uggt2 |
T |
A |
14: 119,296,521 (GRCm39) |
Y447F |
possibly damaging |
Het |
| Zfp160 |
G |
A |
17: 21,245,911 (GRCm39) |
V154I |
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 |
|
R3792:Kdm4b
|
UTSW |
17 |
56,662,944 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3897:Kdm4b
|
UTSW |
17 |
56,703,955 (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'- GAGCCTAAGCAGCCCTAATGTG -3'
(R):5'- ATCAGGTCTTCCCATGGCTC -3'
Sequencing Primer
(F):5'- TAAGCAGCCCTAATGTGACCTTAGG -3'
(R):5'- TGGCACTCACCAGGACTTAG -3'
|
| Posted On |
2015-01-23 |
Incidental Mutation