Incidental Mutation 'R2135:Kdm4a'
| ID |
235703 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| MMRRC Submission |
040138-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.643)
|
| Stock # |
R2135 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 117999656 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Proline
at position 922
(L922P)
|
| 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: L922P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: L922P
| 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: L922P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: L922P
| 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: L922P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: L922P
| 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: L922P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: L922P
| 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 |
0.9187 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.6%
|
| Validation Efficiency |
100% (70/70) |
| 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: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930522L14Rik |
A |
T |
5: 109,885,509 (GRCm39) |
H116Q |
probably benign |
Het |
| Adamts16 |
C |
A |
13: 70,949,126 (GRCm39) |
L178F |
probably damaging |
Het |
| Adgrv1 |
A |
G |
13: 81,672,676 (GRCm39) |
|
probably null |
Het |
| Akap9 |
A |
G |
5: 4,114,509 (GRCm39) |
T46A |
probably damaging |
Het |
| Ankrd2 |
T |
C |
19: 42,032,498 (GRCm39) |
L253P |
probably damaging |
Het |
| Arap3 |
T |
C |
18: 38,107,509 (GRCm39) |
D1336G |
probably damaging |
Het |
| Cacna2d2 |
C |
A |
9: 107,403,712 (GRCm39) |
L992I |
possibly damaging |
Het |
| Cdhr2 |
T |
A |
13: 54,868,760 (GRCm39) |
I574N |
probably damaging |
Het |
| Cecr2 |
C |
T |
6: 120,697,923 (GRCm39) |
T74M |
probably damaging |
Het |
| Ces5a |
C |
A |
8: 94,226,369 (GRCm39) |
E481D |
probably benign |
Het |
| Cfap74 |
C |
G |
4: 155,514,397 (GRCm39) |
N544K |
probably damaging |
Het |
| Cfap74 |
T |
A |
4: 155,514,408 (GRCm39) |
L548Q |
probably damaging |
Het |
| Cfb |
C |
T |
17: 35,076,254 (GRCm39) |
V1145I |
possibly damaging |
Het |
| CK137956 |
A |
G |
4: 127,845,433 (GRCm39) |
|
probably benign |
Het |
| Commd10 |
T |
A |
18: 47,123,604 (GRCm39) |
L153Q |
possibly damaging |
Het |
| Cox6c |
T |
C |
15: 35,937,429 (GRCm39) |
|
probably benign |
Het |
| Dock4 |
A |
G |
12: 40,795,667 (GRCm39) |
Y828C |
probably benign |
Het |
| Ermp1 |
T |
C |
19: 29,623,465 (GRCm39) |
D119G |
possibly damaging |
Het |
| Ext1 |
G |
T |
15: 52,965,140 (GRCm39) |
Q409K |
possibly damaging |
Het |
| Fat4 |
A |
T |
3: 39,034,882 (GRCm39) |
I2845F |
probably damaging |
Het |
| Frmd6 |
A |
G |
12: 70,941,771 (GRCm39) |
N494S |
probably benign |
Het |
| Fscn3 |
A |
G |
6: 28,431,583 (GRCm39) |
T305A |
probably benign |
Het |
| Gbx1 |
G |
T |
5: 24,731,220 (GRCm39) |
R199S |
possibly damaging |
Het |
| Gm11437 |
T |
C |
11: 84,044,638 (GRCm39) |
R192G |
probably damaging |
Het |
| Gucy2c |
T |
A |
6: 136,700,726 (GRCm39) |
D572V |
probably damaging |
Het |
| Idh1 |
A |
C |
1: 65,201,078 (GRCm39) |
M291R |
probably damaging |
Het |
| Kcnt2 |
A |
G |
1: 140,356,551 (GRCm39) |
Y330C |
probably damaging |
Het |
| L3mbtl2 |
A |
G |
15: 81,566,215 (GRCm39) |
D346G |
possibly damaging |
Het |
| Lsm14a |
A |
G |
7: 34,070,609 (GRCm39) |
S96P |
probably damaging |
Het |
| Ltn1 |
A |
G |
16: 87,179,601 (GRCm39) |
L1520P |
probably damaging |
Het |
| Marchf6 |
A |
T |
15: 31,509,910 (GRCm39) |
C26* |
probably null |
Het |
| Msra |
G |
A |
14: 64,360,657 (GRCm39) |
P228L |
probably damaging |
Het |
| Mycbp2 |
A |
T |
14: 103,383,378 (GRCm39) |
D395E |
probably benign |
Het |
| Mycbp2 |
T |
C |
14: 103,446,329 (GRCm39) |
Y1800C |
probably damaging |
Het |
| Ncr1 |
C |
A |
7: 4,343,756 (GRCm39) |
|
probably benign |
Het |
| Nkd1 |
T |
C |
8: 89,318,278 (GRCm39) |
I201T |
probably benign |
Het |
| Nsrp1 |
A |
T |
11: 76,945,834 (GRCm39) |
|
probably benign |
Het |
| Or2t48 |
A |
C |
11: 58,420,611 (GRCm39) |
I67S |
probably damaging |
Het |
| Or7e177 |
T |
A |
9: 20,211,593 (GRCm39) |
D32E |
probably benign |
Het |
| Pate5 |
A |
C |
9: 35,750,479 (GRCm39) |
|
probably null |
Het |
| Pkdrej |
T |
C |
15: 85,700,707 (GRCm39) |
Y1743C |
probably damaging |
Het |
| Plekha5 |
T |
A |
6: 140,526,225 (GRCm39) |
H281Q |
possibly damaging |
Het |
| Ppp2r3d |
A |
C |
9: 101,088,757 (GRCm39) |
M522R |
probably damaging |
Het |
| Prdm12 |
T |
C |
2: 31,530,325 (GRCm39) |
F72S |
possibly damaging |
Het |
| Prima1 |
A |
T |
12: 103,168,949 (GRCm39) |
F106L |
probably damaging |
Het |
| Ptchd4 |
A |
G |
17: 42,627,965 (GRCm39) |
H142R |
probably benign |
Het |
| Rasgrf2 |
G |
A |
13: 92,120,374 (GRCm39) |
A793V |
probably benign |
Het |
| Rbsn |
T |
A |
6: 92,166,854 (GRCm39) |
M597L |
probably benign |
Het |
| Ripk4 |
A |
T |
16: 97,544,933 (GRCm39) |
D571E |
probably damaging |
Het |
| Rp9 |
T |
C |
9: 22,379,425 (GRCm39) |
K25E |
possibly damaging |
Het |
| Sec31b |
T |
C |
19: 44,523,135 (GRCm39) |
S211G |
probably damaging |
Het |
| Shank2 |
C |
T |
7: 143,964,971 (GRCm39) |
P1070S |
probably damaging |
Het |
| Sla |
A |
G |
15: 66,654,563 (GRCm39) |
V241A |
probably benign |
Het |
| Slc25a40 |
A |
G |
5: 8,477,489 (GRCm39) |
T25A |
possibly damaging |
Het |
| Slc3a2 |
A |
G |
19: 8,685,608 (GRCm39) |
S164P |
probably benign |
Het |
| Slc7a5 |
A |
T |
8: 122,610,444 (GRCm39) |
W457R |
probably null |
Het |
| Slco6c1 |
A |
G |
1: 97,032,542 (GRCm39) |
M303T |
probably benign |
Het |
| Smim10l1 |
T |
C |
6: 133,082,489 (GRCm39) |
F12S |
probably damaging |
Het |
| Syne2 |
A |
G |
12: 75,999,560 (GRCm39) |
I2318V |
probably damaging |
Het |
| Tecta |
A |
C |
9: 42,251,581 (GRCm39) |
C1781G |
probably damaging |
Het |
| Timmdc1 |
A |
T |
16: 38,319,313 (GRCm39) |
H280Q |
probably benign |
Het |
| Tktl2 |
G |
A |
8: 66,964,999 (GRCm39) |
V186M |
probably damaging |
Het |
| Tmem30b |
A |
G |
12: 73,592,107 (GRCm39) |
L336P |
probably damaging |
Het |
| Tmem94 |
A |
G |
11: 115,685,575 (GRCm39) |
I943V |
probably benign |
Het |
| Tshb |
A |
G |
3: 102,685,464 (GRCm39) |
|
probably null |
Het |
| Vcpip1 |
A |
G |
1: 9,818,035 (GRCm39) |
V116A |
probably benign |
Het |
| Vmn2r76 |
A |
G |
7: 85,880,219 (GRCm39) |
Y156H |
probably benign |
Het |
| Zcrb1 |
T |
C |
15: 93,295,067 (GRCm39) |
N23S |
probably damaging |
Het |
| Zfyve26 |
T |
C |
12: 79,292,826 (GRCm39) |
R2108G |
possibly 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 |
|
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'- TCTGTTTGGAAACTGACCAGGG -3'
(R):5'- GTGTCTGGAAAGGCCTGTTC -3'
Sequencing Primer
(F):5'- AACTGACCAGGGGCAGGC -3'
(R):5'- GGCCTGTTCTGCCTTCCATTTG -3'
|
| Posted On |
2014-10-01 |
Incidental Mutation