Incidental Mutation 'IGL02673:Kdm4a'
| ID |
303008 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.631)
|
| Stock # |
IGL02673
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
4 |
| Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 118025769 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Asparagine
at position 146
(D146N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000062910
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000050288]
[ENSMUST00000097911]
[ENSMUST00000106403]
[ENSMUST00000106406]
|
| AlphaFold |
Q8BW72 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000050288
AA Change: D146N
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: D146N
| 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
AA Change: D146N
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: D146N
| 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
AA Change: D146N
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: D146N
| 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
AA Change: D146N
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: D146N
| 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
|
| Coding Region Coverage |
|
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9930012K11Rik |
T |
A |
14: 70,395,056 (GRCm39) |
T33S |
probably benign |
Het |
| Abca4 |
T |
C |
3: 121,897,150 (GRCm39) |
Y610H |
probably damaging |
Het |
| Agl |
A |
T |
3: 116,575,248 (GRCm39) |
C630S |
probably benign |
Het |
| Alkbh6 |
G |
T |
7: 30,013,536 (GRCm39) |
G202C |
probably damaging |
Het |
| Ascc3 |
A |
T |
10: 50,536,769 (GRCm39) |
M701L |
probably benign |
Het |
| Bpgm |
T |
A |
6: 34,464,769 (GRCm39) |
L162Q |
probably damaging |
Het |
| Ccdc150 |
A |
G |
1: 54,368,149 (GRCm39) |
T592A |
probably benign |
Het |
| Chpf2 |
G |
A |
5: 24,796,302 (GRCm39) |
R416Q |
probably benign |
Het |
| Col14a1 |
G |
A |
15: 55,282,178 (GRCm39) |
G813E |
unknown |
Het |
| Col18a1 |
C |
T |
10: 76,894,997 (GRCm39) |
G983D |
probably damaging |
Het |
| Col5a1 |
C |
T |
2: 27,864,727 (GRCm39) |
A737V |
unknown |
Het |
| Cyp2a22 |
T |
G |
7: 26,637,525 (GRCm39) |
K157Q |
probably benign |
Het |
| Dhx57 |
A |
G |
17: 80,574,974 (GRCm39) |
V668A |
probably damaging |
Het |
| Eps8l1 |
T |
A |
7: 4,481,731 (GRCm39) |
V743E |
probably damaging |
Het |
| Fnbp4 |
C |
T |
2: 90,593,816 (GRCm39) |
T557M |
probably benign |
Het |
| Fzd5 |
C |
T |
1: 64,774,265 (GRCm39) |
E499K |
possibly damaging |
Het |
| Gm57858 |
A |
C |
3: 36,100,848 (GRCm39) |
|
probably benign |
Het |
| Il1r2 |
A |
G |
1: 40,154,323 (GRCm39) |
Y230C |
probably damaging |
Het |
| Insrr |
A |
C |
3: 87,720,368 (GRCm39) |
E1002A |
possibly damaging |
Het |
| Kidins220 |
G |
A |
12: 25,044,991 (GRCm39) |
V262M |
probably damaging |
Het |
| Kif26b |
C |
T |
1: 178,649,170 (GRCm39) |
P430L |
probably damaging |
Het |
| Mamdc4 |
T |
C |
2: 25,460,066 (GRCm39) |
S62G |
probably benign |
Het |
| Mcu |
C |
A |
10: 59,303,466 (GRCm39) |
V124F |
probably damaging |
Het |
| Mlf1 |
A |
G |
3: 67,301,280 (GRCm39) |
M98V |
probably benign |
Het |
| Mogs |
T |
C |
6: 83,095,199 (GRCm39) |
V672A |
probably damaging |
Het |
| Ntrk3 |
T |
C |
7: 77,900,512 (GRCm39) |
D609G |
probably damaging |
Het |
| Or1n1 |
C |
T |
2: 36,750,188 (GRCm39) |
M57I |
probably benign |
Het |
| Pdlim5 |
T |
A |
3: 142,058,548 (GRCm39) |
E65D |
probably damaging |
Het |
| Peg3 |
T |
C |
7: 6,713,413 (GRCm39) |
N603S |
probably damaging |
Het |
| Pkd1 |
A |
G |
17: 24,790,257 (GRCm39) |
Y980C |
probably benign |
Het |
| Rack1 |
A |
G |
11: 48,691,357 (GRCm39) |
T23A |
probably benign |
Het |
| Rad50 |
A |
T |
11: 53,579,067 (GRCm39) |
I497K |
probably benign |
Het |
| Sin3a |
C |
A |
9: 57,014,725 (GRCm39) |
Q649K |
probably damaging |
Het |
| Sirt6 |
A |
G |
10: 81,461,671 (GRCm39) |
F46L |
probably damaging |
Het |
| Slc40a1 |
A |
T |
1: 45,957,576 (GRCm39) |
I136N |
possibly damaging |
Het |
| Sspo |
G |
A |
6: 48,452,794 (GRCm39) |
R2834H |
probably damaging |
Het |
| Sspo |
G |
T |
6: 48,475,709 (GRCm39) |
|
probably null |
Het |
| Sycp2 |
T |
A |
2: 178,036,004 (GRCm39) |
T228S |
possibly damaging |
Het |
| Uhrf2 |
T |
A |
19: 30,070,207 (GRCm39) |
N785K |
probably damaging |
Het |
| Vmn2r58 |
T |
A |
7: 41,514,082 (GRCm39) |
Y187F |
possibly damaging |
Het |
| Vmn2r80 |
A |
G |
10: 79,005,318 (GRCm39) |
I318M |
probably benign |
Het |
| Vps13c |
T |
C |
9: 67,785,380 (GRCm39) |
L249P |
probably damaging |
Het |
| Zw10 |
T |
A |
9: 48,988,893 (GRCm39) |
|
probably null |
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 |
|
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 |
|
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 |
|
|
| Posted On |
2015-04-16 |
Incidental Mutation