Incidental Mutation 'R5115:Kdm4a'
| ID |
394144 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| MMRRC Submission |
042703-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.643)
|
| Stock # |
R5115 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 118019778 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Glutamine
at position 326
(P326Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000062910
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000050288]
[ENSMUST00000097911]
[ENSMUST00000106403]
[ENSMUST00000106406]
|
| AlphaFold |
Q8BW72 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000050288
AA Change: P326Q
PolyPhen 2
Score 0.749 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: P326Q
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
13 |
55 |
1.01e-20 |
SMART |
|
JmjC
|
142 |
308 |
3.57e-63 |
SMART |
|
low complexity region
|
461 |
487 |
N/A |
INTRINSIC |
|
low complexity region
|
502 |
525 |
N/A |
INTRINSIC |
|
low complexity region
|
619 |
637 |
N/A |
INTRINSIC |
|
PHD
|
709 |
767 |
4.93e-4 |
SMART |
|
PHD
|
829 |
885 |
1.54e-5 |
SMART |
|
TUDOR
|
897 |
954 |
2.87e-8 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000097911
AA Change: P326Q
PolyPhen 2
Score 0.578 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: P326Q
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
13 |
55 |
1.01e-20 |
SMART |
|
JmjC
|
142 |
308 |
3.57e-63 |
SMART |
|
low complexity region
|
461 |
487 |
N/A |
INTRINSIC |
|
low complexity region
|
502 |
525 |
N/A |
INTRINSIC |
|
low complexity region
|
619 |
637 |
N/A |
INTRINSIC |
|
PHD
|
709 |
767 |
4.93e-4 |
SMART |
|
PHD
|
829 |
885 |
1.54e-5 |
SMART |
|
TUDOR
|
897 |
954 |
2.41e-10 |
SMART |
|
TUDOR
|
955 |
1011 |
4.77e-14 |
SMART |
|
low complexity region
|
1032 |
1044 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000106403
AA Change: P326Q
PolyPhen 2
Score 0.578 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: P326Q
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
13 |
55 |
1.01e-20 |
SMART |
|
JmjC
|
142 |
308 |
3.57e-63 |
SMART |
|
low complexity region
|
461 |
487 |
N/A |
INTRINSIC |
|
low complexity region
|
502 |
525 |
N/A |
INTRINSIC |
|
low complexity region
|
619 |
637 |
N/A |
INTRINSIC |
|
PHD
|
709 |
767 |
4.93e-4 |
SMART |
|
PHD
|
829 |
885 |
1.54e-5 |
SMART |
|
TUDOR
|
897 |
954 |
2.41e-10 |
SMART |
|
TUDOR
|
955 |
1011 |
4.77e-14 |
SMART |
|
low complexity region
|
1032 |
1044 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000106406
AA Change: P326Q
PolyPhen 2
Score 0.578 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: P326Q
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
13 |
55 |
1.01e-20 |
SMART |
|
JmjC
|
142 |
308 |
3.57e-63 |
SMART |
|
low complexity region
|
461 |
487 |
N/A |
INTRINSIC |
|
low complexity region
|
502 |
525 |
N/A |
INTRINSIC |
|
low complexity region
|
619 |
637 |
N/A |
INTRINSIC |
|
PHD
|
709 |
767 |
4.93e-4 |
SMART |
|
PHD
|
829 |
885 |
1.54e-5 |
SMART |
|
TUDOR
|
897 |
954 |
2.41e-10 |
SMART |
|
TUDOR
|
955 |
1011 |
4.77e-14 |
SMART |
|
low complexity region
|
1032 |
1044 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000157678
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000164821
|
| Meta Mutation Damage Score |
0.3092 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.0%
- 10x: 95.2%
- 20x: 88.2%
|
| Validation Efficiency |
100% (47/47) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein containing a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demethylase, converting specific trimethylated histone residues to the dimethylated form, and as a transcriptional repressor. [provided by RefSeq, Apr 2009]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 31 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acsl6 |
C |
T |
11: 54,231,324 (GRCm39) |
|
probably null |
Het |
| Asic1 |
C |
T |
15: 99,569,933 (GRCm39) |
L85F |
probably damaging |
Het |
| Atic |
G |
A |
1: 71,596,434 (GRCm39) |
|
probably null |
Het |
| Atp1b2 |
T |
C |
11: 69,494,299 (GRCm39) |
T65A |
probably damaging |
Het |
| C2cd6 |
T |
A |
1: 59,090,420 (GRCm39) |
I446L |
probably benign |
Het |
| Cep83 |
A |
G |
10: 94,604,751 (GRCm39) |
H488R |
probably benign |
Het |
| Cwc15 |
A |
G |
9: 14,419,192 (GRCm39) |
I163V |
probably benign |
Het |
| Cyp11b2 |
A |
T |
15: 74,727,277 (GRCm39) |
|
probably null |
Het |
| Fat2 |
A |
G |
11: 55,187,159 (GRCm39) |
V1229A |
probably damaging |
Het |
| Fbn1 |
T |
C |
2: 125,174,303 (GRCm39) |
D1851G |
probably damaging |
Het |
| Golga7 |
A |
T |
8: 23,735,986 (GRCm39) |
|
probably null |
Het |
| Gsdmc2 |
A |
T |
15: 63,699,617 (GRCm39) |
H270Q |
probably benign |
Het |
| Kng1 |
G |
A |
16: 22,888,032 (GRCm39) |
R209H |
possibly damaging |
Het |
| Mfn1 |
T |
C |
3: 32,618,456 (GRCm39) |
|
probably null |
Het |
| Mllt6 |
G |
A |
11: 97,560,326 (GRCm39) |
S210N |
possibly damaging |
Het |
| Nlrc5 |
G |
A |
8: 95,203,447 (GRCm39) |
V516I |
possibly damaging |
Het |
| Nrbp1 |
T |
G |
5: 31,401,059 (GRCm39) |
Y96* |
probably null |
Het |
| Papola |
T |
C |
12: 105,793,219 (GRCm39) |
V513A |
probably benign |
Het |
| Pikfyve |
T |
C |
1: 65,263,276 (GRCm39) |
|
probably benign |
Het |
| Plin1 |
AGGCCACCAGGGGGTGGGC |
AGGC |
7: 79,379,692 (GRCm39) |
|
probably benign |
Het |
| Prkdc |
A |
G |
16: 15,608,444 (GRCm39) |
Q3082R |
probably benign |
Het |
| Rbfox1 |
A |
G |
16: 7,227,636 (GRCm39) |
S405G |
probably damaging |
Het |
| Recql |
T |
C |
6: 142,304,285 (GRCm39) |
|
probably benign |
Het |
| Serpina3c |
T |
C |
12: 104,113,651 (GRCm39) |
E365G |
probably damaging |
Het |
| Slc17a5 |
A |
G |
9: 78,484,394 (GRCm39) |
V122A |
probably benign |
Het |
| Sprr2b |
G |
T |
3: 92,224,862 (GRCm39) |
C36F |
unknown |
Het |
| Stk36 |
T |
C |
1: 74,674,986 (GRCm39) |
I1307T |
probably damaging |
Het |
| Tmc6 |
G |
A |
11: 117,666,014 (GRCm39) |
T300I |
probably damaging |
Het |
| Ttll9 |
C |
A |
2: 152,831,510 (GRCm39) |
|
probably benign |
Het |
| Vmn1r71 |
T |
A |
7: 10,481,885 (GRCm39) |
M202L |
probably benign |
Het |
| Zfp276 |
A |
G |
8: 123,991,716 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Kdm4a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01670:Kdm4a
|
APN |
4 |
118,017,698 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01845:Kdm4a
|
APN |
4 |
118,017,656 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
IGL02009:Kdm4a
|
APN |
4 |
118,017,366 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL02296:Kdm4a
|
APN |
4 |
118,034,662 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02366:Kdm4a
|
APN |
4 |
118,017,703 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
IGL02606:Kdm4a
|
APN |
4 |
118,017,486 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02673:Kdm4a
|
APN |
4 |
118,025,769 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0245:Kdm4a
|
UTSW |
4 |
118,032,886 (GRCm39) |
missense |
probably benign |
0.05 |
|
R0326:Kdm4a
|
UTSW |
4 |
118,018,903 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0551:Kdm4a
|
UTSW |
4 |
117,995,428 (GRCm39) |
makesense |
probably null |
|
|
R0603:Kdm4a
|
UTSW |
4 |
117,999,708 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0652:Kdm4a
|
UTSW |
4 |
118,032,886 (GRCm39) |
missense |
probably benign |
0.05 |
|
R0799:Kdm4a
|
UTSW |
4 |
118,004,189 (GRCm39) |
splice site |
probably null |
|
|
R0847:Kdm4a
|
UTSW |
4 |
118,021,695 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R1307:Kdm4a
|
UTSW |
4 |
118,032,839 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1572:Kdm4a
|
UTSW |
4 |
117,996,146 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R1869:Kdm4a
|
UTSW |
4 |
117,996,068 (GRCm39) |
missense |
probably null |
1.00 |
|
R1902:Kdm4a
|
UTSW |
4 |
118,017,596 (GRCm39) |
missense |
probably benign |
0.38 |
|
R1903:Kdm4a
|
UTSW |
4 |
118,017,596 (GRCm39) |
missense |
probably benign |
0.38 |
|
R2135:Kdm4a
|
UTSW |
4 |
117,999,656 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3856:Kdm4a
|
UTSW |
4 |
118,010,428 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4687:Kdm4a
|
UTSW |
4 |
118,001,280 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4940:Kdm4a
|
UTSW |
4 |
118,018,951 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5229:Kdm4a
|
UTSW |
4 |
118,003,802 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5305:Kdm4a
|
UTSW |
4 |
118,017,698 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5423:Kdm4a
|
UTSW |
4 |
117,996,105 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5750:Kdm4a
|
UTSW |
4 |
117,999,396 (GRCm39) |
intron |
probably benign |
|
|
R5849:Kdm4a
|
UTSW |
4 |
118,019,037 (GRCm39) |
missense |
probably benign |
0.17 |
|
R5876:Kdm4a
|
UTSW |
4 |
117,996,073 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6564:Kdm4a
|
UTSW |
4 |
118,034,636 (GRCm39) |
missense |
probably benign |
0.18 |
|
R6772:Kdm4a
|
UTSW |
4 |
117,999,752 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R6982:Kdm4a
|
UTSW |
4 |
118,010,636 (GRCm39) |
splice site |
probably null |
|
|
R7410:Kdm4a
|
UTSW |
4 |
118,001,115 (GRCm39) |
missense |
possibly damaging |
0.64 |
|
R7418:Kdm4a
|
UTSW |
4 |
118,017,440 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8808:Kdm4a
|
UTSW |
4 |
117,999,480 (GRCm39) |
missense |
unknown |
|
|
R8956:Kdm4a
|
UTSW |
4 |
118,019,013 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R8958:Kdm4a
|
UTSW |
4 |
117,999,573 (GRCm39) |
missense |
probably benign |
0.08 |
|
R9233:Kdm4a
|
UTSW |
4 |
118,004,193 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9281:Kdm4a
|
UTSW |
4 |
117,995,728 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9647:Kdm4a
|
UTSW |
4 |
118,017,399 (GRCm39) |
missense |
probably benign |
|
|
R9647:Kdm4a
|
UTSW |
4 |
118,003,790 (GRCm39) |
missense |
probably benign |
0.01 |
|
Z1176:Kdm4a
|
UTSW |
4 |
118,034,699 (GRCm39) |
missense |
probably benign |
0.41 |
|
Z1176:Kdm4a
|
UTSW |
4 |
118,010,387 (GRCm39) |
missense |
probably benign |
0.00 |
|
Z1177:Kdm4a
|
UTSW |
4 |
118,004,366 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TTCCTTCCCCAGAGCTAAGC -3'
(R):5'- GCCCCAACAATGTGATTTTAAACC -3'
Sequencing Primer
(F):5'- ACAGCCCACCCTGTACCTTC -3'
(R):5'- ACCTTCTAATGCTTGAATCACAC -3'
|
| Posted On |
2016-06-15 |
Incidental Mutation