Incidental Mutation 'R0847:Kdm4a'
| ID |
77003 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| MMRRC Submission |
039026-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.631)
|
| Stock # |
R0847 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
4 |
| Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 118021695 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Lysine
at position 266
(E266K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000062910
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000050288]
[ENSMUST00000097911]
[ENSMUST00000106403]
[ENSMUST00000106406]
|
| AlphaFold |
Q8BW72 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000050288
AA Change: E266K
PolyPhen 2
Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: E266K
| 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: E266K
PolyPhen 2
Score 0.911 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: E266K
| 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: E266K
PolyPhen 2
Score 0.911 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: E266K
| 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: E266K
PolyPhen 2
Score 0.911 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: E266K
| 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
|
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.4%
- 20x: 95.2%
|
| Validation Efficiency |
|
| 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: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb1b |
T |
C |
5: 8,895,764 (GRCm39) |
I899T |
probably damaging |
Het |
| Ahnak |
C |
T |
19: 8,983,797 (GRCm39) |
Q1694* |
probably null |
Het |
| Cblc |
A |
T |
7: 19,524,459 (GRCm39) |
Y260* |
probably null |
Het |
| Ccn4 |
T |
G |
15: 66,791,124 (GRCm39) |
C309G |
probably damaging |
Het |
| Ceacam5 |
A |
G |
7: 17,491,762 (GRCm39) |
T711A |
possibly damaging |
Het |
| Cep63 |
A |
G |
9: 102,465,957 (GRCm39) |
S690P |
probably benign |
Het |
| Chia1 |
A |
T |
3: 106,039,253 (GRCm39) |
I448F |
probably benign |
Het |
| Dmxl2 |
A |
T |
9: 54,313,112 (GRCm39) |
F1712I |
probably damaging |
Het |
| Ecpas |
G |
A |
4: 58,841,439 (GRCm39) |
T645I |
probably benign |
Het |
| Exosc3 |
A |
G |
4: 45,319,695 (GRCm39) |
V109A |
probably damaging |
Het |
| Fxyd7 |
A |
G |
7: 30,744,029 (GRCm39) |
C60R |
probably damaging |
Het |
| Gm17349 |
C |
A |
15: 99,600,289 (GRCm39) |
|
probably benign |
Het |
| Gpn2 |
A |
G |
4: 133,315,906 (GRCm39) |
N199D |
probably benign |
Het |
| Ints12 |
C |
T |
3: 132,814,603 (GRCm39) |
T270M |
possibly damaging |
Het |
| Kremen2 |
G |
T |
17: 23,963,634 (GRCm39) |
T50N |
probably damaging |
Het |
| Macf1 |
A |
T |
4: 123,293,159 (GRCm39) |
D1249E |
probably benign |
Het |
| Mdga2 |
T |
A |
12: 66,769,854 (GRCm39) |
K146N |
probably damaging |
Het |
| Med20 |
G |
A |
17: 47,922,618 (GRCm39) |
|
probably null |
Het |
| Myo18b |
T |
C |
5: 113,022,354 (GRCm39) |
|
probably benign |
Het |
| Nav3 |
T |
A |
10: 109,739,718 (GRCm39) |
T84S |
possibly damaging |
Het |
| Olfm2 |
A |
G |
9: 20,579,953 (GRCm39) |
V266A |
probably damaging |
Het |
| Or5b101 |
A |
T |
19: 13,005,095 (GRCm39) |
Y199* |
probably null |
Het |
| Or5b123 |
C |
T |
19: 13,596,915 (GRCm39) |
H87Y |
probably benign |
Het |
| Or6c69b |
T |
A |
10: 129,627,327 (GRCm39) |
I44F |
probably damaging |
Het |
| Pthlh |
A |
T |
6: 147,164,766 (GRCm39) |
|
probably null |
Het |
| Rpap3 |
C |
T |
15: 97,601,082 (GRCm39) |
|
probably null |
Het |
| Rprd2 |
A |
G |
3: 95,672,725 (GRCm39) |
S893P |
probably benign |
Het |
| Sacm1l |
G |
A |
9: 123,377,927 (GRCm39) |
G69D |
probably damaging |
Het |
| Slc27a4 |
T |
C |
2: 29,701,261 (GRCm39) |
S351P |
probably benign |
Het |
| Sobp |
C |
G |
10: 42,898,415 (GRCm39) |
R390P |
probably damaging |
Het |
| Spata7 |
T |
A |
12: 98,614,689 (GRCm39) |
M107K |
possibly damaging |
Het |
| Sri |
G |
A |
5: 8,113,755 (GRCm39) |
|
probably null |
Het |
| Stab2 |
T |
C |
10: 86,805,735 (GRCm39) |
I204V |
probably benign |
Het |
| Synm |
T |
C |
7: 67,384,804 (GRCm39) |
I511V |
probably damaging |
Het |
| Tbr1 |
T |
C |
2: 61,635,373 (GRCm39) |
S108P |
probably benign |
Het |
| Tln1 |
A |
G |
4: 43,555,333 (GRCm39) |
F197S |
probably damaging |
Het |
| Tmem167b |
C |
T |
3: 108,467,537 (GRCm39) |
G46R |
probably benign |
Het |
| Tmprss11g |
T |
C |
5: 86,638,585 (GRCm39) |
K301R |
probably benign |
Het |
| Tnfrsf21 |
C |
T |
17: 43,349,104 (GRCm39) |
H239Y |
probably benign |
Het |
| Trpm2 |
C |
T |
10: 77,765,122 (GRCm39) |
V960M |
possibly damaging |
Het |
| Ube3a |
G |
A |
7: 58,926,334 (GRCm39) |
D371N |
possibly damaging |
Het |
| Vmn2r57 |
A |
T |
7: 41,078,225 (GRCm39) |
F78I |
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 |
|
|
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 |
|
R5115:Kdm4a
|
UTSW |
4 |
118,019,778 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
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'- AATAGCAGCCTCCTTGGAAGTGTTC -3'
(R):5'- TCAAGACCTGGCAGTCTCCACTTAC -3'
Sequencing Primer
(F):5'- CTTAAATGGGTCGCCCTAGAG -3'
(R):5'- AGTCTCCACTTACCCCTGG -3'
|
| Posted On |
2013-10-16 |
Incidental Mutation