Incidental Mutation 'IGL01670:Kdm4a'
ID |
103464 |
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: 0.643)
|
Stock # |
IGL01670
|
Quality Score |
|
Status
|
|
Chromosome |
4 |
Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 118017698 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Tyrosine to Cysteine
at position 456
(Y456C)
|
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: Y456C
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000062910 Gene: ENSMUSG00000033326 AA Change: Y456C
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: Y456C
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000095524 Gene: ENSMUSG00000033326 AA Change: Y456C
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: Y456C
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000102011 Gene: ENSMUSG00000033326 AA Change: Y456C
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: Y456C
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000102014 Gene: ENSMUSG00000033326 AA Change: Y456C
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
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000164821
|
Meta Mutation Damage Score |
0.0747 |
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: 46 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acy1 |
A |
C |
9: 106,314,006 (GRCm39) |
|
probably benign |
Het |
Add1 |
C |
A |
5: 34,777,407 (GRCm39) |
Q57K |
probably damaging |
Het |
Alms1 |
A |
G |
6: 85,655,132 (GRCm39) |
E3226G |
probably benign |
Het |
Arl1 |
G |
T |
10: 88,577,884 (GRCm39) |
R151L |
probably damaging |
Het |
Cabs1 |
T |
A |
5: 88,127,869 (GRCm39) |
D173E |
possibly damaging |
Het |
Cdc34b |
T |
C |
11: 94,632,845 (GRCm39) |
L15P |
probably benign |
Het |
Cdyl2 |
A |
G |
8: 117,351,092 (GRCm39) |
V13A |
probably damaging |
Het |
Chd7 |
G |
T |
4: 8,827,033 (GRCm39) |
R1026L |
probably damaging |
Het |
Cldn34b4 |
T |
C |
X: 75,441,195 (GRCm39) |
S151P |
probably damaging |
Het |
Col14a1 |
T |
A |
15: 55,192,662 (GRCm39) |
I25N |
unknown |
Het |
Crisp4 |
T |
A |
1: 18,198,901 (GRCm39) |
T178S |
probably benign |
Het |
Csmd2 |
C |
T |
4: 128,407,164 (GRCm39) |
|
probably benign |
Het |
Csmd3 |
T |
G |
15: 47,475,225 (GRCm39) |
N2454H |
probably damaging |
Het |
Cytip |
A |
T |
2: 58,023,785 (GRCm39) |
I345N |
probably damaging |
Het |
Frem2 |
A |
T |
3: 53,564,358 (GRCm39) |
S50T |
possibly damaging |
Het |
Gm9747 |
C |
T |
1: 82,211,870 (GRCm39) |
|
probably benign |
Het |
Gpr37 |
A |
G |
6: 25,669,833 (GRCm39) |
F337S |
probably damaging |
Het |
Herc1 |
A |
G |
9: 66,394,342 (GRCm39) |
E4182G |
probably damaging |
Het |
Isyna1 |
C |
T |
8: 71,049,706 (GRCm39) |
P511L |
probably benign |
Het |
Kera |
A |
T |
10: 97,444,939 (GRCm39) |
R99S |
possibly damaging |
Het |
Larp7-ps |
T |
C |
4: 92,079,737 (GRCm39) |
|
probably null |
Het |
Mcm2 |
A |
G |
6: 88,864,614 (GRCm39) |
|
probably benign |
Het |
Myl12a |
T |
C |
17: 71,303,848 (GRCm39) |
T10A |
probably benign |
Het |
Nav3 |
A |
G |
10: 109,550,102 (GRCm39) |
V1876A |
possibly damaging |
Het |
Nkx6-1 |
T |
A |
5: 101,809,806 (GRCm39) |
Q247L |
probably benign |
Het |
Nol8 |
A |
C |
13: 49,814,784 (GRCm39) |
K297N |
possibly damaging |
Het |
Or4c119 |
T |
A |
2: 88,987,261 (GRCm39) |
Y86F |
probably benign |
Het |
Or51e1 |
A |
T |
7: 102,358,772 (GRCm39) |
Q102L |
probably damaging |
Het |
Or5w18 |
A |
G |
2: 87,633,224 (GRCm39) |
T164A |
probably benign |
Het |
Pard3b |
A |
T |
1: 62,250,807 (GRCm39) |
N579Y |
probably damaging |
Het |
Pdcd11 |
T |
A |
19: 47,094,743 (GRCm39) |
L509H |
probably damaging |
Het |
Prss29 |
T |
C |
17: 25,541,437 (GRCm39) |
S266P |
probably benign |
Het |
Rapgef3 |
G |
T |
15: 97,647,543 (GRCm39) |
H766N |
probably benign |
Het |
Rasa1 |
A |
T |
13: 85,373,609 (GRCm39) |
S818T |
probably damaging |
Het |
Rtn4ip1 |
A |
G |
10: 43,804,322 (GRCm39) |
M1V |
probably null |
Het |
Sall1 |
A |
T |
8: 89,758,199 (GRCm39) |
V635D |
probably benign |
Het |
Slc35b4 |
C |
T |
6: 34,147,484 (GRCm39) |
V35I |
probably benign |
Het |
Slc5a11 |
G |
A |
7: 122,869,172 (GRCm39) |
A587T |
probably benign |
Het |
Slc6a21 |
T |
C |
7: 44,937,557 (GRCm39) |
V616A |
possibly damaging |
Het |
Sorl1 |
A |
G |
9: 41,912,788 (GRCm39) |
S1398P |
possibly damaging |
Het |
Srcap |
A |
G |
7: 127,127,604 (GRCm39) |
K390E |
probably damaging |
Het |
Sycp2 |
C |
T |
2: 178,019,843 (GRCm39) |
E558K |
probably benign |
Het |
Tcf20 |
T |
C |
15: 82,739,564 (GRCm39) |
N629S |
possibly damaging |
Het |
Tmem154 |
A |
G |
3: 84,591,537 (GRCm39) |
Y29C |
probably damaging |
Het |
Tmtc3 |
A |
G |
10: 100,282,987 (GRCm39) |
I856T |
probably benign |
Het |
Zswim6 |
A |
G |
13: 107,865,101 (GRCm39) |
|
noncoding transcript |
Het |
|
Other mutations in Kdm4a |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
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 |
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 |
2014-01-21 |