Incidental Mutation 'R4506:Kdm2b'
| ID |
332010 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm2b
|
| Ensembl Gene |
ENSMUSG00000029475 |
| Gene Name |
lysine (K)-specific demethylase 2B |
| Synonyms |
Jhdm1b, Fbxl10, Cxxc2 |
| MMRRC Submission |
041584-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4506 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
122870665-122989823 bp(-) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 122888625 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 589
(T589A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000083376
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031435]
[ENSMUST00000046073]
[ENSMUST00000086200]
[ENSMUST00000118027]
[ENSMUST00000121739]
[ENSMUST00000127403]
[ENSMUST00000152872]
|
| AlphaFold |
Q6P1G2 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000031435
AA Change: T62A
PolyPhen 2
Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000031435
Gene: ENSMUSG00000029475
AA Change: T62A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:zf-CXXC
|
45 |
91 |
1.6e-17 |
PFAM |
|
PHD
|
101 |
163 |
8.58e-4 |
SMART |
|
low complexity region
|
259 |
290 |
N/A |
INTRINSIC |
|
low complexity region
|
370 |
380 |
N/A |
INTRINSIC |
|
low complexity region
|
457 |
473 |
N/A |
INTRINSIC |
|
low complexity region
|
485 |
499 |
N/A |
INTRINSIC |
|
FBOX
|
505 |
545 |
1.69e-2 |
SMART |
|
LRR
|
588 |
610 |
1.31e2 |
SMART |
|
LRR
|
612 |
637 |
2.9e2 |
SMART |
|
LRR
|
652 |
676 |
2.04e2 |
SMART |
|
LRR
|
677 |
702 |
1.1e1 |
SMART |
|
LRR
|
732 |
757 |
3.91e1 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000046073
AA Change: T595A
PolyPhen 2
Score 0.462 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000038229
Gene: ENSMUSG00000029475
AA Change: T595A
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:JmjC
|
23 |
101 |
4e-41 |
BLAST |
|
JmjC
|
147 |
315 |
3.61e-41 |
SMART |
|
low complexity region
|
380 |
401 |
N/A |
INTRINSIC |
|
low complexity region
|
406 |
424 |
N/A |
INTRINSIC |
|
PDB:2YU2|A
|
472 |
546 |
1e-17 |
PDB |
|
Pfam:zf-CXXC
|
578 |
624 |
3e-17 |
PFAM |
|
PHD
|
634 |
696 |
8.58e-4 |
SMART |
|
low complexity region
|
792 |
823 |
N/A |
INTRINSIC |
|
low complexity region
|
903 |
913 |
N/A |
INTRINSIC |
|
low complexity region
|
990 |
1006 |
N/A |
INTRINSIC |
|
low complexity region
|
1018 |
1032 |
N/A |
INTRINSIC |
|
FBOX
|
1038 |
1078 |
1.69e-2 |
SMART |
|
LRR
|
1121 |
1143 |
1.31e2 |
SMART |
|
LRR
|
1145 |
1170 |
2.9e2 |
SMART |
|
LRR
|
1185 |
1209 |
2.04e2 |
SMART |
|
LRR
|
1210 |
1235 |
1.1e1 |
SMART |
|
LRR
|
1265 |
1290 |
3.91e1 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000086200
AA Change: T589A
PolyPhen 2
Score 0.584 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000083376
Gene: ENSMUSG00000029475
AA Change: T589A
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:JmjC
|
17 |
95 |
4e-41 |
BLAST |
|
JmjC
|
141 |
309 |
3.61e-41 |
SMART |
|
low complexity region
|
374 |
395 |
N/A |
INTRINSIC |
|
low complexity region
|
400 |
418 |
N/A |
INTRINSIC |
|
PDB:2YU2|A
|
466 |
540 |
1e-17 |
PDB |
|
Pfam:zf-CXXC
|
572 |
618 |
2.1e-17 |
PFAM |
|
PHD
|
628 |
690 |
8.58e-4 |
SMART |
|
low complexity region
|
786 |
817 |
N/A |
INTRINSIC |
|
low complexity region
|
897 |
907 |
N/A |
INTRINSIC |
|
low complexity region
|
984 |
1000 |
N/A |
INTRINSIC |
|
low complexity region
|
1012 |
1026 |
N/A |
INTRINSIC |
|
FBOX
|
1032 |
1072 |
1.69e-2 |
SMART |
|
LRR
|
1115 |
1137 |
1.31e2 |
SMART |
|
LRR
|
1139 |
1164 |
2.9e2 |
SMART |
|
LRR
|
1179 |
1203 |
2.04e2 |
SMART |
|
LRR
|
1204 |
1229 |
1.1e1 |
SMART |
|
LRR
|
1259 |
1284 |
3.91e1 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000118027
AA Change: T595A
PolyPhen 2
Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000114052
Gene: ENSMUSG00000029475
AA Change: T595A
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:JmjC
|
23 |
101 |
4e-41 |
BLAST |
|
JmjC
|
147 |
315 |
3.61e-41 |
SMART |
|
low complexity region
|
380 |
401 |
N/A |
INTRINSIC |
|
low complexity region
|
406 |
424 |
N/A |
INTRINSIC |
|
PDB:2YU2|A
|
472 |
546 |
9e-18 |
PDB |
|
Pfam:zf-CXXC
|
578 |
624 |
2.1e-17 |
PFAM |
|
PHD
|
634 |
696 |
8.58e-4 |
SMART |
|
low complexity region
|
865 |
875 |
N/A |
INTRINSIC |
|
low complexity region
|
952 |
968 |
N/A |
INTRINSIC |
|
low complexity region
|
980 |
994 |
N/A |
INTRINSIC |
|
FBOX
|
1000 |
1040 |
1.69e-2 |
SMART |
|
LRR
|
1083 |
1105 |
1.31e2 |
SMART |
|
LRR
|
1107 |
1132 |
2.9e2 |
SMART |
|
LRR
|
1147 |
1171 |
2.04e2 |
SMART |
|
LRR
|
1172 |
1197 |
1.1e1 |
SMART |
|
LRR
|
1227 |
1252 |
3.91e1 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000121739
AA Change: T540A
PolyPhen 2
Score 0.129 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000114049
Gene: ENSMUSG00000029475
AA Change: T540A
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:JmjC
|
1 |
46 |
2e-19 |
BLAST |
|
JmjC
|
92 |
260 |
3.61e-41 |
SMART |
|
low complexity region
|
325 |
346 |
N/A |
INTRINSIC |
|
low complexity region
|
351 |
369 |
N/A |
INTRINSIC |
|
PDB:2YU2|A
|
417 |
491 |
1e-17 |
PDB |
|
Pfam:zf-CXXC
|
523 |
569 |
5.4e-17 |
PFAM |
|
PHD
|
579 |
641 |
8.58e-4 |
SMART |
|
low complexity region
|
737 |
768 |
N/A |
INTRINSIC |
|
low complexity region
|
848 |
858 |
N/A |
INTRINSIC |
|
low complexity region
|
935 |
951 |
N/A |
INTRINSIC |
|
low complexity region
|
963 |
977 |
N/A |
INTRINSIC |
|
FBOX
|
983 |
1023 |
1.69e-2 |
SMART |
|
LRR
|
1066 |
1088 |
1.31e2 |
SMART |
|
LRR
|
1090 |
1115 |
2.9e2 |
SMART |
|
LRR
|
1130 |
1154 |
2.04e2 |
SMART |
|
LRR
|
1155 |
1180 |
1.1e1 |
SMART |
|
LRR
|
1210 |
1235 |
3.91e1 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123479
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000127403
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129998
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000152872
|
| SMART Domains |
Protein: ENSMUSP00000119746
Gene: ENSMUSG00000029475
| Domain | Start | End | E-Value | Type |
|---|
|
PHD
|
25 |
87 |
8.58e-4 |
SMART |
|
low complexity region
|
243 |
253 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173355
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174357
|
| Meta Mutation Damage Score |
0.1070 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.8%
|
| Validation Efficiency |
98% (42/43) |
| MGI Phenotype |
FUNCTION: The protein encoded by this gene is a H3K36-specific histone demethylase, which contains an N-terminal jumonji C domain, a CxxC zinc finger domain, a plant homeodomain finger, an F-box, and eight leucine-rich repeats. Amongst its demonstrated functions, this protein plays roles in the suppression of premature cellular senescence, leukemia maintenance and development, maintenance of mouse embryonic stem cell pluripotency, and induced pluripotent stem cell generation. Mice homozygous for a targeted deletion of the zinc finger domain display embryonic lethality with development ceasing at approximately 7 to 8 days post coitum, demonstrating an essential role in early development. A pseudogene of this gene is found on chromosome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
PHENOTYPE: Mice homozygous for a targeted allele that does not express the long form protein exhibit exencephaly, fetal and postnatal lethality, coloboma, curly tail, oligozoospermia, increased apoptosis, and increased neuronal precursor proliferation. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700012B07Rik |
G |
T |
11: 109,794,261 |
P137T |
probably damaging |
Het |
| Abcc5 |
A |
T |
16: 20,333,695 |
I1367N |
probably damaging |
Het |
| Ace |
T |
A |
11: 105,976,666 |
L152Q |
probably damaging |
Het |
| Adam19 |
G |
A |
11: 46,118,444 |
D232N |
possibly damaging |
Het |
| Anapc4 |
A |
T |
5: 52,835,730 |
N61I |
possibly damaging |
Het |
| Ap5m1 |
T |
C |
14: 49,073,761 |
V96A |
probably damaging |
Het |
| Atr |
T |
A |
9: 95,865,237 |
C191S |
probably benign |
Het |
| Carmil3 |
GGACGA |
GGA |
14: 55,499,476 |
|
probably benign |
Het |
| Cnot6l |
A |
T |
5: 96,086,174 |
V326E |
possibly damaging |
Het |
| Fcer2a |
A |
T |
8: 3,688,603 |
|
probably null |
Het |
| Fgfr3 |
A |
G |
5: 33,729,999 |
T221A |
probably damaging |
Het |
| Gm6632 |
C |
T |
5: 59,054,478 |
|
noncoding transcript |
Het |
| Gm8909 |
A |
T |
17: 36,161,480 |
|
probably benign |
Het |
| Gpr158 |
T |
A |
2: 21,826,999 |
M970K |
probably damaging |
Het |
| Ip6k3 |
A |
T |
17: 27,145,180 |
L298Q |
possibly damaging |
Het |
| Itpr1 |
A |
G |
6: 108,432,686 |
D1727G |
probably damaging |
Het |
| Krtcap2 |
A |
G |
3: 89,246,256 |
|
probably benign |
Het |
| Map3k13 |
A |
G |
16: 21,922,178 |
S752G |
probably benign |
Het |
| Mvb12a |
G |
T |
8: 71,543,459 |
A86S |
probably benign |
Het |
| Nktr |
T |
A |
9: 121,748,883 |
|
probably benign |
Het |
| Olfr160 |
C |
T |
9: 37,711,464 |
V272I |
probably benign |
Het |
| Olfr393 |
A |
T |
11: 73,847,695 |
C143* |
probably null |
Het |
| Parp4 |
T |
A |
14: 56,652,304 |
N1847K |
unknown |
Het |
| Pcdhga8 |
G |
C |
18: 37,816,763 |
V411L |
probably damaging |
Het |
| Piwil4 |
T |
C |
9: 14,725,963 |
T352A |
probably damaging |
Het |
| Ric8a |
A |
G |
7: 140,858,516 |
I223V |
probably benign |
Het |
| Slc25a51 |
C |
T |
4: 45,399,768 |
V141M |
probably benign |
Het |
| Slc7a5 |
A |
T |
8: 121,887,495 |
|
probably null |
Het |
| Slc7a9 |
A |
T |
7: 35,453,420 |
T88S |
probably damaging |
Het |
| Tbrg1 |
T |
A |
9: 37,654,395 |
E87V |
probably damaging |
Het |
| Tnfsf4 |
T |
C |
1: 161,417,174 |
S145P |
probably damaging |
Het |
| Tomm34 |
C |
A |
2: 164,054,372 |
|
probably null |
Het |
| Trpv3 |
A |
G |
11: 73,295,324 |
N647S |
probably benign |
Het |
| Upf1 |
G |
A |
8: 70,337,566 |
R637C |
probably damaging |
Het |
| Vmn2r23 |
A |
T |
6: 123,702,925 |
Q35H |
probably damaging |
Het |
| Wdtc1 |
C |
T |
4: 133,308,819 |
V137M |
probably damaging |
Het |
| Zfp276 |
G |
A |
8: 123,264,927 |
|
probably null |
Het |
| Zfp90 |
C |
T |
8: 106,424,864 |
P403L |
possibly damaging |
Het |
|
| Other mutations in Kdm2b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00578:Kdm2b
|
APN |
5 |
122961567 |
missense |
probably damaging |
1.00 |
|
IGL02061:Kdm2b
|
APN |
5 |
122883341 |
missense |
probably damaging |
1.00 |
|
IGL02142:Kdm2b
|
APN |
5 |
122947835 |
missense |
probably damaging |
0.99 |
|
IGL02143:Kdm2b
|
APN |
5 |
122947835 |
missense |
probably damaging |
0.99 |
|
IGL02147:Kdm2b
|
APN |
5 |
122947835 |
missense |
probably damaging |
0.99 |
|
IGL02294:Kdm2b
|
APN |
5 |
122961474 |
missense |
probably damaging |
1.00 |
|
IGL02309:Kdm2b
|
APN |
5 |
122947820 |
missense |
probably damaging |
0.99 |
|
IGL03039:Kdm2b
|
APN |
5 |
122881671 |
missense |
probably benign |
0.06 |
|
IGL03134:Kdm2b
|
UTSW |
5 |
122932674 |
missense |
probably damaging |
1.00 |
|
PIT4520001:Kdm2b
|
UTSW |
5 |
122941047 |
missense |
probably damaging |
1.00 |
|
R0008:Kdm2b
|
UTSW |
5 |
122881743 |
missense |
probably benign |
0.08 |
|
R0592:Kdm2b
|
UTSW |
5 |
122961134 |
splice site |
probably benign |
|
|
R0894:Kdm2b
|
UTSW |
5 |
122984460 |
critical splice donor site |
probably null |
|
|
R1078:Kdm2b
|
UTSW |
5 |
122961541 |
missense |
possibly damaging |
0.83 |
|
R1387:Kdm2b
|
UTSW |
5 |
122880268 |
missense |
probably damaging |
1.00 |
|
R1441:Kdm2b
|
UTSW |
5 |
122932880 |
missense |
probably benign |
0.25 |
|
R1550:Kdm2b
|
UTSW |
5 |
122881057 |
missense |
probably damaging |
1.00 |
|
R1795:Kdm2b
|
UTSW |
5 |
122984460 |
critical splice donor site |
probably null |
|
|
R2060:Kdm2b
|
UTSW |
5 |
122883365 |
missense |
probably damaging |
1.00 |
|
R2161:Kdm2b
|
UTSW |
5 |
122880699 |
missense |
probably damaging |
1.00 |
|
R2259:Kdm2b
|
UTSW |
5 |
122882416 |
missense |
probably damaging |
1.00 |
|
R3843:Kdm2b
|
UTSW |
5 |
122934793 |
missense |
probably damaging |
0.98 |
|
R3844:Kdm2b
|
UTSW |
5 |
122934793 |
missense |
probably damaging |
0.98 |
|
R3859:Kdm2b
|
UTSW |
5 |
122880227 |
missense |
probably damaging |
1.00 |
|
R4680:Kdm2b
|
UTSW |
5 |
122934786 |
missense |
probably damaging |
0.99 |
|
R4786:Kdm2b
|
UTSW |
5 |
122880854 |
critical splice acceptor site |
probably null |
|
|
R4894:Kdm2b
|
UTSW |
5 |
122940967 |
nonsense |
probably null |
|
|
R5265:Kdm2b
|
UTSW |
5 |
122878588 |
missense |
probably damaging |
1.00 |
|
R5522:Kdm2b
|
UTSW |
5 |
122949162 |
missense |
probably damaging |
1.00 |
|
R5746:Kdm2b
|
UTSW |
5 |
122879364 |
missense |
probably damaging |
1.00 |
|
R5813:Kdm2b
|
UTSW |
5 |
122871868 |
missense |
probably benign |
0.37 |
|
R5920:Kdm2b
|
UTSW |
5 |
122880296 |
missense |
probably damaging |
1.00 |
|
R5961:Kdm2b
|
UTSW |
5 |
122932661 |
missense |
probably benign |
0.37 |
|
R6029:Kdm2b
|
UTSW |
5 |
122879587 |
missense |
probably damaging |
1.00 |
|
R6280:Kdm2b
|
UTSW |
5 |
122878624 |
missense |
probably damaging |
1.00 |
|
R6303:Kdm2b
|
UTSW |
5 |
122881744 |
missense |
probably benign |
0.34 |
|
R6304:Kdm2b
|
UTSW |
5 |
122881744 |
missense |
probably benign |
0.34 |
|
R6383:Kdm2b
|
UTSW |
5 |
122934778 |
missense |
probably damaging |
1.00 |
|
R6432:Kdm2b
|
UTSW |
5 |
122880191 |
missense |
probably damaging |
1.00 |
|
R6513:Kdm2b
|
UTSW |
5 |
122880239 |
missense |
probably damaging |
0.99 |
|
R6526:Kdm2b
|
UTSW |
5 |
122961469 |
missense |
probably damaging |
1.00 |
|
R7213:Kdm2b
|
UTSW |
5 |
122921469 |
missense |
probably damaging |
0.99 |
|
R7226:Kdm2b
|
UTSW |
5 |
122921449 |
missense |
possibly damaging |
0.60 |
|
R7292:Kdm2b
|
UTSW |
5 |
122880791 |
missense |
probably damaging |
0.98 |
|
R7893:Kdm2b
|
UTSW |
5 |
122947739 |
missense |
probably benign |
0.12 |
|
R8021:Kdm2b
|
UTSW |
5 |
122932919 |
missense |
probably damaging |
0.99 |
|
R8038:Kdm2b
|
UTSW |
5 |
122960895 |
intron |
probably benign |
|
|
R8162:Kdm2b
|
UTSW |
5 |
122934793 |
missense |
probably damaging |
0.98 |
|
R8397:Kdm2b
|
UTSW |
5 |
122880516 |
missense |
probably benign |
0.03 |
|
R8411:Kdm2b
|
UTSW |
5 |
122880176 |
missense |
probably damaging |
1.00 |
|
R8899:Kdm2b
|
UTSW |
5 |
122987788 |
nonsense |
probably null |
|
|
R8997:Kdm2b
|
UTSW |
5 |
122880173 |
missense |
probably null |
0.99 |
|
R9142:Kdm2b
|
UTSW |
5 |
122989049 |
unclassified |
probably benign |
|
|
R9192:Kdm2b
|
UTSW |
5 |
122932616 |
missense |
probably benign |
0.05 |
|
R9238:Kdm2b
|
UTSW |
5 |
122871826 |
missense |
probably damaging |
0.98 |
|
R9455:Kdm2b
|
UTSW |
5 |
122961474 |
missense |
probably damaging |
1.00 |
|
R9644:Kdm2b
|
UTSW |
5 |
122982779 |
missense |
probably damaging |
0.98 |
|
R9731:Kdm2b
|
UTSW |
5 |
122987760 |
missense |
probably benign |
0.03 |
|
Z1177:Kdm2b
|
UTSW |
5 |
122880797 |
missense |
probably damaging |
0.98 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCACAGTCAAGACAGGCTGC -3'
(R):5'- TGCTTGACTGCCCCTGAATC -3'
Sequencing Primer
(F):5'- GCCCTGACCTCTTTAATAGGG -3'
(R):5'- GACTGCCCCTGAATCCTCCC -3'
|
| Posted On |
2015-07-21 |
Incidental Mutation