Incidental Mutation 'R3856:Kdm4a'
| ID |
276150 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| MMRRC Submission |
040902-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.643)
|
| Stock # |
R3856 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 118010428 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Histidine
at position 605
(R605H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000102014
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000050288]
[ENSMUST00000097911]
[ENSMUST00000106403]
[ENSMUST00000106406]
|
| AlphaFold |
Q8BW72 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000050288
AA Change: R605H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: R605H
| 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 |
probably damaging
Transcript: ENSMUST00000097911
AA Change: R605H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: R605H
| 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 |
probably damaging
Transcript: ENSMUST00000106403
AA Change: R605H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: R605H
| 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 |
probably damaging
Transcript: ENSMUST00000106406
AA Change: R605H
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: R605H
| 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: ENSMUST00000164821
|
| Meta Mutation Damage Score |
0.0970 |
| Coding Region Coverage |
- 1x: 99.6%
- 3x: 98.7%
- 10x: 96.7%
- 20x: 92.4%
|
| Validation Efficiency |
100% (57/57) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acod1 |
T |
C |
14: 103,292,882 (GRCm39) |
S469P |
possibly damaging |
Het |
| Adgrf5 |
A |
T |
17: 43,757,927 (GRCm39) |
N787I |
possibly damaging |
Het |
| Ank2 |
T |
C |
3: 126,723,493 (GRCm39) |
T945A |
probably benign |
Het |
| Aox4 |
T |
A |
1: 58,293,093 (GRCm39) |
I863N |
probably damaging |
Het |
| Ap3d1 |
A |
G |
10: 80,548,019 (GRCm39) |
I891T |
probably benign |
Het |
| Apex1 |
A |
G |
14: 51,163,714 (GRCm39) |
T109A |
probably benign |
Het |
| Arhgef1 |
G |
A |
7: 24,618,697 (GRCm39) |
G107S |
probably damaging |
Het |
| Atxn7l1 |
A |
G |
12: 33,417,599 (GRCm39) |
T587A |
probably damaging |
Het |
| Atxn7l3 |
T |
C |
11: 102,184,729 (GRCm39) |
D128G |
probably damaging |
Het |
| Cacna1h |
T |
C |
17: 25,611,427 (GRCm39) |
Y457C |
probably damaging |
Het |
| Ccdc60 |
A |
C |
5: 116,310,514 (GRCm39) |
C183G |
probably damaging |
Het |
| Cep131 |
G |
A |
11: 119,958,011 (GRCm39) |
R772* |
probably null |
Het |
| Cnst |
C |
T |
1: 179,407,279 (GRCm39) |
P109S |
probably benign |
Het |
| Crtc2 |
G |
T |
3: 90,169,877 (GRCm39) |
L509F |
probably damaging |
Het |
| Ctsr |
A |
T |
13: 61,309,750 (GRCm39) |
I153N |
possibly damaging |
Het |
| Dffa |
A |
T |
4: 149,188,708 (GRCm39) |
M1L |
possibly damaging |
Het |
| Dnajc16 |
G |
A |
4: 141,490,964 (GRCm39) |
R729* |
probably null |
Het |
| Eef2k |
T |
A |
7: 120,498,594 (GRCm39) |
C91* |
probably null |
Het |
| Eml5 |
T |
C |
12: 98,782,283 (GRCm39) |
D1336G |
probably damaging |
Het |
| F12 |
G |
A |
13: 55,569,035 (GRCm39) |
|
probably null |
Het |
| Fam43b |
G |
C |
4: 138,122,409 (GRCm39) |
R304G |
probably benign |
Het |
| Fbxo40 |
A |
T |
16: 36,789,445 (GRCm39) |
L555Q |
probably damaging |
Het |
| Frmpd1 |
T |
C |
4: 45,283,698 (GRCm39) |
S840P |
probably damaging |
Het |
| Gadd45a |
C |
T |
6: 67,013,989 (GRCm39) |
|
probably null |
Het |
| Galnt7 |
T |
C |
8: 57,985,658 (GRCm39) |
|
probably benign |
Het |
| Gm5592 |
G |
A |
7: 40,807,259 (GRCm39) |
|
probably benign |
Het |
| Gpr171 |
T |
C |
3: 59,005,506 (GRCm39) |
T90A |
probably damaging |
Het |
| Gpr82 |
A |
T |
X: 13,531,577 (GRCm39) |
T42S |
probably benign |
Het |
| H2-M10.6 |
T |
A |
17: 37,123,396 (GRCm39) |
I30N |
probably benign |
Het |
| Hk2 |
T |
C |
6: 82,713,657 (GRCm39) |
E447G |
possibly damaging |
Het |
| Hspa4l |
C |
A |
3: 40,739,821 (GRCm39) |
H698Q |
probably benign |
Het |
| Idi1 |
G |
T |
13: 8,935,968 (GRCm39) |
A25S |
probably benign |
Het |
| Nhlrc2 |
T |
C |
19: 56,576,703 (GRCm39) |
|
probably null |
Het |
| Nt5c2 |
A |
G |
19: 46,884,957 (GRCm39) |
V252A |
probably damaging |
Het |
| Or52ae7 |
T |
A |
7: 103,119,867 (GRCm39) |
V207E |
probably damaging |
Het |
| Pbp2 |
A |
G |
6: 135,287,143 (GRCm39) |
L68P |
probably benign |
Het |
| Pcnx3 |
G |
T |
19: 5,728,995 (GRCm39) |
T547K |
probably benign |
Het |
| Ppp1r12a |
T |
C |
10: 108,089,362 (GRCm39) |
|
probably benign |
Het |
| Prmt9 |
G |
A |
8: 78,294,894 (GRCm39) |
V413I |
probably benign |
Het |
| Pudp |
T |
C |
18: 50,701,124 (GRCm39) |
N203S |
probably benign |
Het |
| Rnf213 |
T |
C |
11: 119,371,765 (GRCm39) |
|
probably benign |
Het |
| Sall3 |
G |
A |
18: 81,015,717 (GRCm39) |
T737M |
probably damaging |
Het |
| Scn2b |
A |
G |
9: 45,036,759 (GRCm39) |
N89S |
possibly damaging |
Het |
| Sgsm1 |
A |
G |
5: 113,411,125 (GRCm39) |
V580A |
probably benign |
Het |
| Slc13a4 |
C |
A |
6: 35,248,539 (GRCm39) |
|
probably null |
Het |
| Slc4a4 |
A |
C |
5: 89,380,698 (GRCm39) |
S1015R |
probably benign |
Het |
| Slc8a1 |
T |
C |
17: 81,955,803 (GRCm39) |
T412A |
probably benign |
Het |
| Spag17 |
A |
T |
3: 100,014,075 (GRCm39) |
D2116V |
probably damaging |
Het |
| Trim55 |
T |
C |
3: 19,727,120 (GRCm39) |
F396L |
probably benign |
Het |
| Usp54 |
C |
A |
14: 20,638,488 (GRCm39) |
M197I |
probably damaging |
Het |
| Vmn1r189 |
A |
T |
13: 22,286,439 (GRCm39) |
F133I |
possibly damaging |
Het |
| Zfp735 |
T |
C |
11: 73,602,282 (GRCm39) |
S409P |
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 |
|
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'- ACCAACCTTGTACCTCCTAGG -3'
(R):5'- AAGCCTTTGTCCTCTAAGCTCAG -3'
Sequencing Primer
(F):5'- ACCTTGTACCTCCTAGGAAGAG -3'
(R):5'- TAAGCTCAGCCTCCCGAGAGAG -3'
|
| Posted On |
2015-04-06 |
Incidental Mutation