Incidental Mutation 'R5876:Kdm4a'
ID |
455519 |
Institutional Source |
Beutler Lab
|
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 # |
R5876 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
4 |
Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 117996073 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Methionine to Isoleucine
at position 985
(M985I)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000102014
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030263]
[ENSMUST00000050288]
[ENSMUST00000097911]
[ENSMUST00000097912]
[ENSMUST00000106403]
[ENSMUST00000106406]
[ENSMUST00000106410]
|
AlphaFold |
Q8BW72 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000030263
|
SMART Domains |
Protein: ENSMUSP00000030263 Gene: ENSMUSG00000028538
Domain | Start | End | E-Value | Type |
transmembrane domain
|
5 |
27 |
N/A |
INTRINSIC |
low complexity region
|
37 |
47 |
N/A |
INTRINSIC |
Pfam:Glyco_transf_29
|
102 |
373 |
5.7e-75 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000050288
|
SMART Domains |
Protein: ENSMUSP00000062910 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 |
2.87e-8 |
SMART |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000097911
AA Change: M985I
PolyPhen 2
Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000095524 Gene: ENSMUSG00000033326 AA Change: M985I
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: ENSMUST00000097912
|
SMART Domains |
Protein: ENSMUSP00000095525 Gene: ENSMUSG00000028538
Domain | Start | End | E-Value | Type |
transmembrane domain
|
5 |
27 |
N/A |
INTRINSIC |
Pfam:Glyco_transf_29
|
86 |
357 |
5.4e-75 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000106403
AA Change: M985I
PolyPhen 2
Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000102011 Gene: ENSMUSG00000033326 AA Change: M985I
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: M985I
PolyPhen 2
Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000102014 Gene: ENSMUSG00000033326 AA Change: M985I
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: ENSMUST00000106410
|
SMART Domains |
Protein: ENSMUSP00000102018 Gene: ENSMUSG00000028538
Domain | Start | End | E-Value | Type |
transmembrane domain
|
5 |
27 |
N/A |
INTRINSIC |
low complexity region
|
37 |
47 |
N/A |
INTRINSIC |
Pfam:Glyco_transf_29
|
106 |
372 |
4.7e-63 |
PFAM |
|
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.9%
- 20x: 93.6%
|
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: 57 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700034E13Rik |
A |
G |
18: 52,796,654 (GRCm39) |
D64G |
possibly damaging |
Het |
Ano2 |
T |
A |
6: 126,016,242 (GRCm39) |
M925K |
possibly damaging |
Het |
Arnt2 |
T |
C |
7: 83,996,720 (GRCm39) |
T69A |
probably damaging |
Het |
Asap2 |
T |
A |
12: 21,262,810 (GRCm39) |
N229K |
possibly damaging |
Het |
Atp13a3 |
T |
A |
16: 30,181,552 (GRCm39) |
N23Y |
probably benign |
Het |
Cbr4 |
G |
A |
8: 61,943,627 (GRCm39) |
G91R |
possibly damaging |
Het |
Cdc27 |
A |
T |
11: 104,406,244 (GRCm39) |
C624S |
probably benign |
Het |
Cdc42bpg |
T |
A |
19: 6,360,845 (GRCm39) |
I201N |
probably damaging |
Het |
Cdh5 |
A |
G |
8: 104,869,209 (GRCm39) |
Y645C |
probably damaging |
Het |
Celsr2 |
C |
T |
3: 108,321,259 (GRCm39) |
V518I |
probably damaging |
Het |
Clca4b |
T |
C |
3: 144,617,821 (GRCm39) |
T761A |
possibly damaging |
Het |
Cpne4 |
C |
A |
9: 104,802,969 (GRCm39) |
S204R |
probably damaging |
Het |
Dcaf1 |
T |
C |
9: 106,740,849 (GRCm39) |
W1279R |
probably damaging |
Het |
Dennd4a |
C |
T |
9: 64,819,037 (GRCm39) |
P1731S |
probably damaging |
Het |
Dmxl1 |
T |
A |
18: 50,004,051 (GRCm39) |
V892D |
possibly damaging |
Het |
Fam131b |
A |
G |
6: 42,298,182 (GRCm39) |
|
probably null |
Het |
Fam83b |
T |
A |
9: 76,399,132 (GRCm39) |
D657V |
possibly damaging |
Het |
Fam83e |
T |
A |
7: 45,371,787 (GRCm39) |
|
probably null |
Het |
Fbxo4 |
A |
T |
15: 4,007,301 (GRCm39) |
I121N |
probably damaging |
Het |
Gabrg2 |
A |
G |
11: 41,859,647 (GRCm39) |
S202P |
probably damaging |
Het |
Grid2 |
T |
A |
6: 64,640,146 (GRCm39) |
I788N |
probably damaging |
Het |
Grik4 |
T |
A |
9: 42,599,319 (GRCm39) |
N53Y |
probably damaging |
Het |
Hipk2 |
A |
C |
6: 38,707,802 (GRCm39) |
|
probably null |
Het |
Hps5 |
T |
C |
7: 46,438,620 (GRCm39) |
T38A |
probably damaging |
Het |
Hs1bp3 |
A |
G |
12: 8,391,843 (GRCm39) |
D315G |
possibly damaging |
Het |
Kdm5d |
A |
G |
Y: 900,525 (GRCm39) |
Y190C |
probably damaging |
Het |
Krt86 |
T |
C |
15: 101,374,491 (GRCm39) |
S295P |
probably damaging |
Het |
Matr3 |
T |
A |
18: 35,720,791 (GRCm39) |
D413E |
probably benign |
Het |
Mbd5 |
T |
A |
2: 49,164,657 (GRCm39) |
F319L |
probably damaging |
Het |
Mcoln1 |
T |
A |
8: 3,560,910 (GRCm39) |
Y411N |
probably damaging |
Het |
Mpdz |
C |
A |
4: 81,203,711 (GRCm39) |
E1863* |
probably null |
Het |
Mrps9 |
A |
G |
1: 42,934,538 (GRCm39) |
E173G |
probably damaging |
Het |
Or7a42 |
A |
T |
10: 78,791,191 (GRCm39) |
I51F |
probably benign |
Het |
Osmr |
T |
C |
15: 6,850,528 (GRCm39) |
T692A |
probably benign |
Het |
Pkhd1l1 |
A |
T |
15: 44,441,984 (GRCm39) |
H3641L |
possibly damaging |
Het |
Pml |
T |
C |
9: 58,140,465 (GRCm39) |
T421A |
possibly damaging |
Het |
Podxl |
A |
G |
6: 31,505,391 (GRCm39) |
|
probably null |
Het |
Ppargc1b |
C |
G |
18: 61,442,164 (GRCm39) |
D591H |
probably damaging |
Het |
Prkag3 |
A |
G |
1: 74,787,975 (GRCm39) |
|
probably benign |
Het |
Proz |
A |
G |
8: 13,123,448 (GRCm39) |
R240G |
probably benign |
Het |
Ptpn13 |
C |
A |
5: 103,624,826 (GRCm39) |
D43E |
probably damaging |
Het |
Rbm5 |
T |
G |
9: 107,637,525 (GRCm39) |
K135N |
probably damaging |
Het |
Ska1 |
G |
A |
18: 74,330,599 (GRCm39) |
T201M |
probably damaging |
Het |
Slc35f5 |
A |
C |
1: 125,515,100 (GRCm39) |
|
probably null |
Het |
Slc9a3 |
T |
C |
13: 74,309,842 (GRCm39) |
L510P |
probably damaging |
Het |
Speer4a2 |
T |
C |
5: 26,289,716 (GRCm39) |
E237G |
probably damaging |
Het |
Svil |
A |
G |
18: 5,082,828 (GRCm39) |
K1231E |
probably damaging |
Het |
Tanc2 |
T |
C |
11: 105,813,439 (GRCm39) |
S1628P |
possibly damaging |
Het |
Tm9sf3 |
T |
A |
19: 41,229,023 (GRCm39) |
D260V |
probably damaging |
Het |
Ttc9 |
G |
T |
12: 81,678,396 (GRCm39) |
R73L |
probably damaging |
Het |
Vps13b |
A |
G |
15: 35,917,207 (GRCm39) |
I3684V |
probably damaging |
Het |
Vps8 |
T |
C |
16: 21,280,189 (GRCm39) |
|
probably null |
Het |
Vwa3b |
T |
A |
1: 37,115,520 (GRCm39) |
I328N |
probably damaging |
Het |
Wdr1 |
C |
T |
5: 38,687,366 (GRCm39) |
V222M |
probably benign |
Het |
Xpnpep1 |
T |
A |
19: 52,985,439 (GRCm39) |
T530S |
probably damaging |
Het |
Zc3h6 |
C |
T |
2: 128,835,197 (GRCm39) |
S111F |
probably benign |
Het |
Zfp768 |
G |
A |
7: 126,943,718 (GRCm39) |
P137S |
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 |
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'- CTCGGTAGTAAGGACTTTCCATG -3'
(R):5'- AGTCCTTCCTGAGTCATTGGC -3'
Sequencing Primer
(F):5'- CTTTCCATGTAAGGAATGACGGCC -3'
(R):5'- CCTGAGTCATTGGCACTTAGC -3'
|
Posted On |
2017-02-10 |