Incidental Mutation 'R5750:Kdm4a'
| ID |
445957 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| MMRRC Submission |
043356-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.643)
|
| Stock # |
R5750 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
| Type of Mutation |
intron |
| DNA Base Change (assembly) |
A to G
at 117999396 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000102014
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000050288]
[ENSMUST00000097911]
[ENSMUST00000106403]
[ENSMUST00000106406]
|
| AlphaFold |
Q8BW72 |
| Predicted Effect |
unknown
Transcript: ENSMUST00000050288
AA Change: F1009L
|
| SMART Domains |
Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: F1009L
| 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 benign
Transcript: ENSMUST00000097911
|
| SMART Domains |
Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
| 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 benign
Transcript: ENSMUST00000106403
|
| SMART Domains |
Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
| 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 benign
Transcript: ENSMUST00000106406
|
| SMART Domains |
Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
| 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: ENSMUST00000152808
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
| Validation Efficiency |
100% (55/55) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Agmat |
G |
A |
4: 141,476,998 (GRCm39) |
V135I |
probably benign |
Het |
| Agr3 |
T |
C |
12: 35,996,941 (GRCm39) |
Y72H |
probably benign |
Het |
| Ankhd1 |
T |
A |
18: 36,757,955 (GRCm39) |
M883K |
probably benign |
Het |
| Cpeb1 |
A |
T |
7: 81,086,099 (GRCm39) |
D9E |
probably benign |
Het |
| Creb3l1 |
C |
T |
2: 91,816,608 (GRCm39) |
V386M |
possibly damaging |
Het |
| Dnlz |
C |
T |
2: 26,241,423 (GRCm39) |
V102M |
probably damaging |
Het |
| Esp4 |
C |
T |
17: 40,913,286 (GRCm39) |
T51M |
probably benign |
Het |
| Fap |
C |
A |
2: 62,359,058 (GRCm39) |
C443F |
probably damaging |
Het |
| Fbxo17 |
G |
A |
7: 28,436,897 (GRCm39) |
R284H |
probably damaging |
Het |
| Fpr1 |
T |
A |
17: 18,097,525 (GRCm39) |
I155F |
probably benign |
Het |
| Fshr |
T |
A |
17: 89,293,669 (GRCm39) |
L336F |
probably benign |
Het |
| Gna15 |
G |
A |
10: 81,345,230 (GRCm39) |
Q212* |
probably null |
Het |
| Hk1 |
A |
G |
10: 62,110,245 (GRCm39) |
F785L |
possibly damaging |
Het |
| Ints8 |
T |
A |
4: 11,241,654 (GRCm39) |
Q263L |
possibly damaging |
Het |
| Itgax |
T |
C |
7: 127,743,878 (GRCm39) |
F880L |
probably benign |
Het |
| Kcnq4 |
A |
C |
4: 120,572,246 (GRCm39) |
V327G |
probably damaging |
Het |
| Leng8 |
C |
T |
7: 4,145,119 (GRCm39) |
S173L |
probably benign |
Het |
| Lrrc37a |
C |
T |
11: 103,348,923 (GRCm39) |
D2591N |
unknown |
Het |
| Macrod2 |
T |
A |
2: 141,357,240 (GRCm39) |
S179T |
probably benign |
Het |
| Map4k2 |
T |
A |
19: 6,401,367 (GRCm39) |
S612R |
probably benign |
Het |
| Mast2 |
A |
G |
4: 116,166,086 (GRCm39) |
|
probably benign |
Het |
| Micall2 |
C |
T |
5: 139,701,456 (GRCm39) |
|
probably null |
Het |
| Miga2 |
T |
A |
2: 30,261,577 (GRCm39) |
W191R |
probably damaging |
Het |
| Mterf1b |
T |
C |
5: 4,246,683 (GRCm39) |
I108T |
probably damaging |
Het |
| Myh2 |
A |
G |
11: 67,082,254 (GRCm39) |
I1319V |
probably benign |
Het |
| Nalcn |
T |
C |
14: 123,809,450 (GRCm39) |
E234G |
probably benign |
Het |
| Ncoa4 |
T |
A |
14: 31,899,264 (GRCm39) |
C602* |
probably null |
Het |
| Ntrk2 |
C |
A |
13: 58,956,736 (GRCm39) |
P65Q |
probably benign |
Het |
| Or52z15 |
G |
A |
7: 103,332,362 (GRCm39) |
V136I |
possibly damaging |
Het |
| Or6c215 |
C |
T |
10: 129,637,489 (GRCm39) |
V302M |
probably benign |
Het |
| P3h1 |
A |
T |
4: 119,095,863 (GRCm39) |
I324F |
probably damaging |
Het |
| Peli2 |
G |
T |
14: 48,493,632 (GRCm39) |
V285L |
possibly damaging |
Het |
| Qser1 |
A |
G |
2: 104,619,268 (GRCm39) |
S515P |
probably damaging |
Het |
| Rnf31 |
C |
T |
14: 55,836,143 (GRCm39) |
R721C |
probably damaging |
Het |
| Rps5 |
A |
G |
7: 12,659,334 (GRCm39) |
K42E |
probably damaging |
Het |
| Rufy4 |
A |
T |
1: 74,172,068 (GRCm39) |
T264S |
probably benign |
Het |
| Shq1 |
A |
T |
6: 100,588,775 (GRCm39) |
V259D |
possibly damaging |
Het |
| Slc22a3 |
T |
C |
17: 12,652,395 (GRCm39) |
I410V |
probably benign |
Het |
| Stx5a |
T |
C |
19: 8,732,501 (GRCm39) |
|
probably benign |
Het |
| Syne1 |
G |
T |
10: 5,289,209 (GRCm39) |
H1430Q |
probably benign |
Het |
| Tasor2 |
G |
A |
13: 3,623,642 (GRCm39) |
Q1421* |
probably null |
Het |
| Tmem126b |
A |
C |
7: 90,118,865 (GRCm39) |
V141G |
probably damaging |
Het |
| Trim52 |
C |
A |
14: 106,344,932 (GRCm39) |
Q197K |
probably benign |
Het |
| Tshz1 |
A |
G |
18: 84,032,086 (GRCm39) |
L774P |
possibly damaging |
Het |
| Ttn |
T |
C |
2: 76,602,031 (GRCm39) |
S10217G |
possibly damaging |
Het |
| Unc45a |
A |
G |
7: 79,984,571 (GRCm39) |
V228A |
probably benign |
Het |
| Unc93a2 |
C |
T |
17: 7,637,130 (GRCm39) |
V133I |
probably benign |
Het |
| Vwa2 |
G |
T |
19: 56,897,663 (GRCm39) |
G656V |
probably benign |
Het |
| Xpo5 |
T |
C |
17: 46,529,556 (GRCm39) |
|
probably null |
Het |
| Zeb2 |
T |
A |
2: 44,887,530 (GRCm39) |
Q494L |
probably damaging |
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 |
|
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 |
|
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'- GAAACAAGGGTTGGATCGTTC -3'
(R):5'- TGTCTGAAAGCGGCTTCTG -3'
Sequencing Primer
(F):5'- TCTACAGAGTGAGTTCCAGGAC -3'
(R):5'- CGGCTTCTGGCAGCACTTTG -3'
|
| Posted On |
2016-11-21 |
Incidental Mutation