Incidental Mutation 'R5700:Kdm4b'
| ID |
450872 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4b
|
| Ensembl Gene |
ENSMUSG00000024201 |
| Gene Name |
lysine (K)-specific demethylase 4B |
| Synonyms |
Jmjd2b, 4732474L06Rik |
| MMRRC Submission |
043328-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5700 (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 56658700 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Threonine
at position 15
(I15T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000118089
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025036]
[ENSMUST00000086835]
[ENSMUST00000139679]
|
| AlphaFold |
Q91VY5 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000025036
AA Change: I15T
PolyPhen 2
Score 0.715 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000025036
Gene: ENSMUSG00000024201
AA Change: I15T
| 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 |
possibly damaging
Transcript: ENSMUST00000086835
AA Change: I15T
PolyPhen 2
Score 0.551 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000084045
Gene: ENSMUSG00000024201
AA Change: I15T
| 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 |
possibly damaging
Transcript: ENSMUST00000139679
AA Change: I15T
PolyPhen 2
Score 0.927 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000118089
Gene: ENSMUSG00000024201
AA Change: I15T
| 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 |
0.9501 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.4%
|
| Validation Efficiency |
98% (50/51) |
| 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: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc2 |
A |
T |
19: 43,786,633 (GRCm39) |
Q155L |
probably benign |
Het |
| Acadvl |
A |
C |
11: 69,904,029 (GRCm39) |
Y242D |
probably damaging |
Het |
| Armc8 |
A |
G |
9: 99,378,202 (GRCm39) |
|
probably null |
Het |
| Barx2 |
A |
T |
9: 31,770,061 (GRCm39) |
F156I |
probably damaging |
Het |
| Best1 |
T |
C |
19: 9,974,563 (GRCm39) |
|
probably benign |
Het |
| Btbd8 |
T |
C |
5: 107,651,514 (GRCm39) |
S136P |
possibly damaging |
Het |
| Btla |
T |
A |
16: 45,070,936 (GRCm39) |
Y298* |
probably null |
Het |
| Casr |
T |
A |
16: 36,329,979 (GRCm39) |
I452F |
probably damaging |
Het |
| Ccser1 |
C |
A |
6: 61,288,260 (GRCm39) |
P141H |
probably benign |
Het |
| Cr2 |
A |
G |
1: 194,842,065 (GRCm39) |
V296A |
probably damaging |
Het |
| Csl |
T |
A |
10: 99,594,877 (GRCm39) |
I63F |
probably damaging |
Het |
| Dbt |
G |
A |
3: 116,313,952 (GRCm39) |
V40M |
probably damaging |
Het |
| Fam53b |
A |
T |
7: 132,361,749 (GRCm39) |
L93Q |
probably damaging |
Het |
| Fdps |
T |
C |
3: 89,002,956 (GRCm39) |
I105V |
probably damaging |
Het |
| Gm4884 |
A |
G |
7: 40,692,643 (GRCm39) |
D204G |
probably benign |
Het |
| Gm5592 |
A |
G |
7: 40,808,003 (GRCm39) |
|
probably benign |
Het |
| Gm7367 |
A |
T |
7: 59,805,510 (GRCm39) |
|
noncoding transcript |
Het |
| Grid2 |
T |
A |
6: 64,071,416 (GRCm39) |
V413D |
possibly damaging |
Het |
| Hgf |
C |
T |
5: 16,815,122 (GRCm39) |
P471L |
probably damaging |
Het |
| Hoxc9 |
T |
C |
15: 102,890,313 (GRCm39) |
Y77H |
possibly damaging |
Het |
| Hs6st3 |
C |
T |
14: 119,376,199 (GRCm39) |
R125* |
probably null |
Het |
| Klhl1 |
T |
C |
14: 96,755,476 (GRCm39) |
N93S |
probably benign |
Het |
| Klhl6 |
G |
A |
16: 19,775,968 (GRCm39) |
Q197* |
probably null |
Het |
| Medag |
T |
C |
5: 149,345,682 (GRCm39) |
V7A |
probably benign |
Het |
| Mptx2 |
G |
A |
1: 173,102,414 (GRCm39) |
L92F |
probably benign |
Het |
| Nckap5 |
C |
T |
1: 125,904,662 (GRCm39) |
|
probably null |
Het |
| Obscn |
T |
C |
11: 59,024,020 (GRCm39) |
K550R |
probably benign |
Het |
| Or2d36 |
A |
G |
7: 106,746,748 (GRCm39) |
N75S |
probably benign |
Het |
| Or2w1b |
T |
A |
13: 21,300,171 (GRCm39) |
V103E |
probably damaging |
Het |
| Or5h25 |
T |
A |
16: 58,930,356 (GRCm39) |
I206F |
probably damaging |
Het |
| Or7a42 |
T |
C |
10: 78,791,318 (GRCm39) |
I93T |
probably damaging |
Het |
| Parp6 |
T |
C |
9: 59,532,010 (GRCm39) |
S101P |
probably damaging |
Het |
| Plcd3 |
T |
C |
11: 102,964,589 (GRCm39) |
N594S |
probably benign |
Het |
| Plscr5 |
A |
T |
9: 92,087,564 (GRCm39) |
K178* |
probably null |
Het |
| Ppp2r1b |
T |
C |
9: 50,789,457 (GRCm39) |
Y443H |
probably damaging |
Het |
| Prnd |
G |
A |
2: 131,795,263 (GRCm39) |
V128I |
probably benign |
Het |
| Rftn1 |
G |
T |
17: 50,309,697 (GRCm39) |
P156Q |
probably damaging |
Het |
| Scmh1 |
T |
C |
4: 120,374,143 (GRCm39) |
V445A |
probably benign |
Het |
| Serpinb6c |
A |
T |
13: 34,083,291 (GRCm39) |
M41K |
probably damaging |
Het |
| Slc66a1 |
C |
T |
4: 139,027,565 (GRCm39) |
S259N |
probably damaging |
Het |
| Spns1 |
A |
G |
7: 125,971,641 (GRCm39) |
V303A |
possibly damaging |
Het |
| Ston1 |
T |
A |
17: 88,951,767 (GRCm39) |
S639R |
probably damaging |
Het |
| Thbs4 |
T |
C |
13: 92,913,461 (GRCm39) |
D153G |
probably benign |
Het |
| Timm44 |
T |
C |
8: 4,324,171 (GRCm39) |
Y36C |
probably damaging |
Het |
| Trim34b |
G |
T |
7: 103,985,618 (GRCm39) |
V418F |
probably damaging |
Het |
| Vmn1r72 |
C |
T |
7: 11,404,350 (GRCm39) |
V33M |
probably damaging |
Het |
| Zcchc7 |
T |
C |
4: 44,931,084 (GRCm39) |
V412A |
probably benign |
Het |
| Zfand1 |
T |
A |
3: 10,406,079 (GRCm39) |
N210I |
probably damaging |
Het |
| Zfhx3 |
A |
G |
8: 109,660,499 (GRCm39) |
H1251R |
probably damaging |
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 |
|
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 |
|
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'- TACTCAACCGGTGTCACCTTG -3'
(R):5'- TCCATGTTTAAGAAGGTCGGGG -3'
Sequencing Primer
(F):5'- CGGTGTCACCTTGGCTTTTGAC -3'
(R):5'- TTTAAGAAGGTCGGGGAGGCAG -3'
|
| Posted On |
2017-01-03 |
Incidental Mutation