Incidental Mutation 'R5423:Kdm4a'
| ID |
426694 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| MMRRC Submission |
042989-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.643)
|
| Stock # |
R5423 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 117996105 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Threonine
at position 975
(A975T)
|
| 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: A975T
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: A975T
| 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: A975T
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: A975T
| 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: A975T
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: A975T
| 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 |
|
| Meta Mutation Damage Score |
0.1550 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
| Validation Efficiency |
98% (60/61) |
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acyp2 |
C |
T |
11: 30,456,354 (GRCm39) |
E98K |
possibly damaging |
Het |
| Adam22 |
C |
A |
5: 8,140,182 (GRCm39) |
G202W |
probably damaging |
Het |
| Adamts9 |
A |
G |
6: 92,857,678 (GRCm39) |
I289T |
possibly damaging |
Het |
| Ak4 |
T |
G |
4: 101,317,760 (GRCm39) |
I110S |
probably damaging |
Het |
| Arhgap9 |
T |
G |
10: 127,165,418 (GRCm39) |
I609S |
probably damaging |
Het |
| Arid4a |
C |
A |
12: 71,116,634 (GRCm39) |
S242* |
probably null |
Het |
| Ceacam1 |
T |
G |
7: 25,173,951 (GRCm39) |
I235L |
probably benign |
Het |
| Chil3 |
T |
C |
3: 106,055,978 (GRCm39) |
D365G |
probably damaging |
Het |
| Ckap2 |
A |
C |
8: 22,667,212 (GRCm39) |
S216R |
probably benign |
Het |
| Cyp2e1 |
G |
T |
7: 140,350,031 (GRCm39) |
V239L |
probably benign |
Het |
| Dnah7b |
T |
A |
1: 46,397,431 (GRCm39) |
M3954K |
probably benign |
Het |
| Ercc6l2 |
A |
T |
13: 64,020,072 (GRCm39) |
|
probably benign |
Het |
| Etv5 |
T |
C |
16: 22,202,404 (GRCm39) |
D468G |
probably damaging |
Het |
| Fbxo44 |
T |
A |
4: 148,238,686 (GRCm39) |
I213F |
probably benign |
Het |
| Gm5084 |
A |
G |
13: 60,360,356 (GRCm39) |
|
noncoding transcript |
Het |
| Gpr17 |
G |
A |
18: 32,080,694 (GRCm39) |
T123I |
probably damaging |
Het |
| Grin3a |
A |
G |
4: 49,770,376 (GRCm39) |
|
probably benign |
Het |
| H2-D1 |
T |
G |
17: 35,484,883 (GRCm39) |
L248R |
probably damaging |
Het |
| Hmcn1 |
T |
C |
1: 150,577,723 (GRCm39) |
I2013V |
probably damaging |
Het |
| Hp1bp3 |
A |
T |
4: 137,953,208 (GRCm39) |
D84V |
probably damaging |
Het |
| Ift140 |
T |
C |
17: 25,252,059 (GRCm39) |
F33S |
probably damaging |
Het |
| Inhbc |
C |
G |
10: 127,193,296 (GRCm39) |
C240S |
probably damaging |
Het |
| Iqgap1 |
T |
A |
7: 80,449,610 (GRCm39) |
E62V |
probably damaging |
Het |
| Kcna4 |
G |
A |
2: 107,126,151 (GRCm39) |
W295* |
probably null |
Het |
| Lrrtm3 |
T |
C |
10: 63,923,931 (GRCm39) |
D412G |
possibly damaging |
Het |
| Midn |
A |
C |
10: 79,991,027 (GRCm39) |
I346L |
probably benign |
Het |
| Ndufa10 |
C |
T |
1: 92,390,042 (GRCm39) |
D259N |
probably benign |
Het |
| Nefh |
C |
A |
11: 4,890,985 (GRCm39) |
A545S |
possibly damaging |
Het |
| Prpf8 |
A |
G |
11: 75,399,784 (GRCm39) |
Y2281C |
probably damaging |
Het |
| Psip1 |
G |
A |
4: 83,378,367 (GRCm39) |
|
probably benign |
Het |
| Ptpro |
G |
T |
6: 137,419,705 (GRCm39) |
A184S |
probably damaging |
Het |
| Rab37 |
T |
A |
11: 115,047,853 (GRCm39) |
I65K |
possibly damaging |
Het |
| Rasgrp4 |
T |
C |
7: 28,844,561 (GRCm39) |
L247P |
probably damaging |
Het |
| Rnf20 |
T |
C |
4: 49,644,620 (GRCm39) |
V295A |
probably damaging |
Het |
| Serpina3g |
A |
G |
12: 104,204,253 (GRCm39) |
|
probably benign |
Het |
| Shox2 |
A |
G |
3: 66,881,087 (GRCm39) |
|
probably benign |
Het |
| Skint6 |
T |
G |
4: 112,707,937 (GRCm39) |
D977A |
possibly damaging |
Het |
| Slc25a23 |
C |
T |
17: 57,360,597 (GRCm39) |
V248M |
probably damaging |
Het |
| Slco1a7 |
T |
A |
6: 141,690,188 (GRCm39) |
K188N |
probably damaging |
Het |
| Smg1 |
A |
T |
7: 117,745,294 (GRCm39) |
D3008E |
possibly damaging |
Het |
| St18 |
A |
G |
1: 6,872,840 (GRCm39) |
S192G |
possibly damaging |
Het |
| Supt20 |
T |
A |
3: 54,616,746 (GRCm39) |
V306E |
probably damaging |
Het |
| T |
T |
C |
17: 8,660,597 (GRCm39) |
Y403H |
probably damaging |
Het |
| Tars3 |
C |
A |
7: 65,333,567 (GRCm39) |
N588K |
probably benign |
Het |
| Tmem132c |
T |
C |
5: 127,640,907 (GRCm39) |
V1026A |
probably benign |
Het |
| Trpv4 |
T |
C |
5: 114,774,506 (GRCm39) |
T193A |
probably benign |
Het |
| Ubqln4 |
A |
G |
3: 88,470,506 (GRCm39) |
N326S |
probably damaging |
Het |
| Uggt2 |
G |
A |
14: 119,256,898 (GRCm39) |
T1112I |
probably damaging |
Het |
| Vasn |
C |
T |
16: 4,466,284 (GRCm39) |
P77L |
probably benign |
Het |
| Vps9d1 |
A |
C |
8: 123,974,704 (GRCm39) |
|
probably null |
Het |
| Washc4 |
C |
A |
10: 83,415,418 (GRCm39) |
Q803K |
possibly damaging |
Het |
| Zcchc2 |
C |
T |
1: 105,958,430 (GRCm39) |
T967I |
probably damaging |
Het |
| Zfp874a |
G |
A |
13: 67,590,473 (GRCm39) |
L404F |
possibly damaging |
Het |
| Zscan30 |
T |
C |
18: 24,104,773 (GRCm39) |
|
noncoding transcript |
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 |
|
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'- GATACCCCAGATCTGTGAAGG -3'
(R):5'- TTTGACGGACCGTACCTTGG -3'
Sequencing Primer
(F):5'- TCTGTGAAGGCACTAAGTGACC -3'
(R):5'- GGACCGTACCTTGGCTTTCAG -3'
|
| Posted On |
2016-09-01 |
Incidental Mutation