Incidental Mutation 'R8808:Kdm4a'
| ID |
672203 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| MMRRC Submission |
068644-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.631)
|
| Stock # |
R8808 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 117999480 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Isoleucine
at position 981
(V981I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000062910
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000050288]
[ENSMUST00000097911]
[ENSMUST00000106403]
[ENSMUST00000106406]
|
| AlphaFold |
Q8BW72 |
| Predicted Effect |
unknown
Transcript: ENSMUST00000050288
AA Change: V981I
|
| SMART Domains |
Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: V981I
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
95% (60/63) |
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
C |
T |
3: 137,775,874 (GRCm39) |
P1688S |
probably benign |
Het |
| 4933412E24Rik |
T |
C |
15: 59,887,919 (GRCm39) |
T174A |
probably benign |
Het |
| Actl10 |
T |
A |
2: 154,395,068 (GRCm39) |
L340Q |
probably damaging |
Het |
| Adra1d |
T |
C |
2: 131,403,397 (GRCm39) |
E231G |
probably damaging |
Het |
| Agt |
T |
A |
8: 125,291,028 (GRCm39) |
D93V |
probably benign |
Het |
| Als2cl |
G |
T |
9: 110,718,282 (GRCm39) |
R341L |
possibly damaging |
Het |
| Ankrd63 |
G |
T |
2: 118,533,549 (GRCm39) |
A124E |
unknown |
Het |
| Aqp8 |
T |
C |
7: 123,065,922 (GRCm39) |
L239P |
probably damaging |
Het |
| Arhgef11 |
A |
G |
3: 87,593,336 (GRCm39) |
E85G |
probably damaging |
Het |
| Cacng4 |
T |
A |
11: 107,685,209 (GRCm39) |
I28F |
possibly damaging |
Het |
| Cc2d1a |
T |
C |
8: 84,861,599 (GRCm39) |
D741G |
probably damaging |
Het |
| Cct8l1 |
T |
A |
5: 25,722,210 (GRCm39) |
N308K |
possibly damaging |
Het |
| Cd300ld2 |
CGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGTCAGAACTGTGGATGGCACAACTGTGCATGGCAGAACTGTGGATGGCACAACTGTGGATGGCAGAACTGTGG |
CGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGTCAGAACTGTGGATGGCACAACTGTGCATGGCAGAACTGTGGATGGCACAACTGTGGATGGCAGAACTGTGG |
11: 114,903,257 (GRCm39) |
|
probably benign |
Het |
| Chrna5 |
T |
A |
9: 54,905,348 (GRCm39) |
D53E |
probably benign |
Het |
| Dap3 |
A |
T |
3: 88,835,514 (GRCm39) |
|
probably null |
Het |
| Disp2 |
A |
G |
2: 118,620,489 (GRCm39) |
Y407C |
probably damaging |
Het |
| Dnah1 |
A |
G |
14: 31,008,771 (GRCm39) |
M2001T |
probably benign |
Het |
| Dysf |
C |
G |
6: 83,996,466 (GRCm39) |
|
probably benign |
Het |
| Eif2ak1 |
A |
T |
5: 143,816,264 (GRCm39) |
K187N |
probably damaging |
Het |
| Ethe1 |
T |
C |
7: 24,294,496 (GRCm39) |
S100P |
probably damaging |
Het |
| Fam186a |
G |
C |
15: 99,842,604 (GRCm39) |
I1213M |
possibly damaging |
Het |
| Gbp9 |
A |
G |
5: 105,232,875 (GRCm39) |
F259S |
probably damaging |
Het |
| Heatr5b |
G |
A |
17: 79,072,834 (GRCm39) |
H1610Y |
possibly damaging |
Het |
| Hk2 |
T |
A |
6: 82,705,747 (GRCm39) |
D852V |
probably benign |
Het |
| Hmcn1 |
T |
A |
1: 150,531,570 (GRCm39) |
Q3233L |
possibly damaging |
Het |
| Htt |
T |
A |
5: 35,046,791 (GRCm39) |
V2369E |
probably benign |
Het |
| Il9 |
C |
A |
13: 56,629,942 (GRCm39) |
E35* |
probably null |
Het |
| Itga8 |
A |
T |
2: 12,137,328 (GRCm39) |
C933* |
probably null |
Het |
| Jak3 |
A |
G |
8: 72,138,164 (GRCm39) |
K872E |
possibly damaging |
Het |
| Kcnmb2 |
A |
C |
3: 32,252,266 (GRCm39) |
M156L |
probably benign |
Het |
| Klhl38 |
A |
T |
15: 58,178,225 (GRCm39) |
*582R |
probably null |
Het |
| Map3k19 |
A |
G |
1: 127,751,866 (GRCm39) |
F495S |
probably damaging |
Het |
| Mpeg1 |
T |
A |
19: 12,440,443 (GRCm39) |
W634R |
probably damaging |
Het |
| Mrpl4 |
T |
A |
9: 20,918,978 (GRCm39) |
Y202N |
possibly damaging |
Het |
| Nme8 |
A |
G |
13: 19,859,978 (GRCm39) |
V214A |
probably damaging |
Het |
| Or4k36 |
A |
T |
2: 111,146,239 (GRCm39) |
R138S |
possibly damaging |
Het |
| Or8k33 |
G |
A |
2: 86,384,297 (GRCm39) |
T57M |
probably damaging |
Het |
| Pcdhgb6 |
A |
G |
18: 37,876,451 (GRCm39) |
I386M |
possibly damaging |
Het |
| Pitpnm1 |
T |
A |
19: 4,162,356 (GRCm39) |
V1062E |
possibly damaging |
Het |
| Plekhm3 |
G |
A |
1: 64,922,355 (GRCm39) |
R607W |
possibly damaging |
Het |
| Plppr2 |
TCGCC |
TC |
9: 21,855,727 (GRCm39) |
|
probably benign |
Het |
| Prap1 |
C |
A |
7: 139,676,982 (GRCm39) |
H141Q |
probably damaging |
Het |
| Prep |
T |
A |
10: 44,971,252 (GRCm39) |
Y187* |
probably null |
Het |
| Rergl |
T |
G |
6: 139,478,865 (GRCm39) |
E3A |
probably benign |
Het |
| Rnf19a |
A |
T |
15: 36,242,021 (GRCm39) |
S673T |
probably benign |
Het |
| Spata31f3 |
TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG |
TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG |
4: 42,871,823 (GRCm39) |
|
probably benign |
Het |
| St18 |
G |
A |
1: 6,880,826 (GRCm39) |
E440K |
probably damaging |
Het |
| Syne1 |
T |
A |
10: 5,309,074 (GRCm39) |
Q645L |
probably damaging |
Het |
| Tmcc1 |
C |
A |
6: 116,111,099 (GRCm39) |
V61L |
|
Het |
| Tmcc1 |
A |
T |
6: 116,111,098 (GRCm39) |
V61E |
|
Het |
| Tmem135 |
G |
C |
7: 88,797,186 (GRCm39) |
L357V |
probably benign |
Het |
| Tmem201 |
C |
A |
4: 149,814,138 (GRCm39) |
R154L |
possibly damaging |
Het |
| Tmem71 |
G |
A |
15: 66,410,655 (GRCm39) |
A239V |
possibly damaging |
Het |
| Tpgs2 |
A |
G |
18: 25,284,275 (GRCm39) |
W78R |
probably damaging |
Het |
| Tssc4 |
T |
C |
7: 142,623,436 (GRCm39) |
V22A |
unknown |
Het |
| Ttn |
T |
A |
2: 76,723,128 (GRCm39) |
E6496D |
unknown |
Het |
| Ttn |
T |
A |
2: 76,697,539 (GRCm39) |
L227F |
|
Het |
| Vps50 |
G |
T |
6: 3,522,338 (GRCm39) |
G169* |
probably null |
Het |
| Yy1 |
CGGCGACCACGGCGGCGGCGGGGGCG |
CGGCG |
12: 108,759,506 (GRCm39) |
|
probably benign |
Het |
| Zfp407 |
T |
C |
18: 84,361,185 (GRCm39) |
K1703R |
probably benign |
Het |
| Zfp616 |
T |
G |
11: 73,976,523 (GRCm39) |
C931G |
probably damaging |
Het |
| Zfp949 |
G |
A |
9: 88,451,417 (GRCm39) |
C329Y |
probably damaging |
Het |
| Zswim5 |
T |
A |
4: 116,822,887 (GRCm39) |
D452E |
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 |
|
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 |
|
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'- ACTGTATCAGCAGCGGTTTGC -3'
(R):5'- TGTGAGGTGGTCAGACTCAC -3'
Sequencing Primer
(F):5'- AGTGTGAGCTTGCATCCTGAAC -3'
(R):5'- TGGTCAGACTCACCACCGAG -3'
|
| Posted On |
2021-04-30 |
Incidental Mutation