Incidental Mutation 'R5305:Kdm4a'
| ID |
404488 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| MMRRC Submission |
042888-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.631)
|
| Stock # |
R5305 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| 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 |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.4%
|
| Validation Efficiency |
99% (67/68) |
| 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 |
|---|
| 4930407I10Rik |
G |
A |
15: 81,943,420 (GRCm39) |
V11M |
possibly damaging |
Het |
| Acot8 |
A |
G |
2: 164,637,685 (GRCm39) |
V179A |
probably benign |
Het |
| Actb |
A |
G |
5: 142,889,985 (GRCm39) |
I194T |
probably benign |
Het |
| Ap1g2 |
A |
G |
14: 55,336,533 (GRCm39) |
V787A |
probably benign |
Het |
| Areg |
G |
T |
5: 91,292,308 (GRCm39) |
A203S |
probably damaging |
Het |
| Asb13 |
A |
T |
13: 3,693,479 (GRCm39) |
D79V |
probably damaging |
Het |
| Atad2b |
C |
T |
12: 5,015,855 (GRCm39) |
T527I |
probably damaging |
Het |
| Auts2 |
T |
G |
5: 131,472,632 (GRCm39) |
|
probably benign |
Het |
| Ceacam3 |
T |
A |
7: 16,885,501 (GRCm39) |
S35T |
probably damaging |
Het |
| Crebzf |
T |
C |
7: 90,093,342 (GRCm39) |
|
probably benign |
Het |
| Cttnbp2 |
G |
T |
6: 18,381,097 (GRCm39) |
N1366K |
probably benign |
Het |
| Cubn |
C |
A |
2: 13,393,750 (GRCm39) |
C1417F |
probably damaging |
Het |
| Dot1l |
C |
T |
10: 80,626,627 (GRCm39) |
P162S |
probably benign |
Het |
| Epc1 |
G |
A |
18: 6,490,690 (GRCm39) |
|
probably benign |
Het |
| Eps8l1 |
A |
G |
7: 4,480,895 (GRCm39) |
S613G |
possibly damaging |
Het |
| Erich6 |
T |
G |
3: 58,532,537 (GRCm39) |
I357L |
probably benign |
Het |
| Foxj3 |
T |
A |
4: 119,477,155 (GRCm39) |
S288T |
possibly damaging |
Het |
| Gls2 |
T |
G |
10: 128,040,578 (GRCm39) |
Y326* |
probably null |
Het |
| Gm11595 |
G |
A |
11: 99,663,381 (GRCm39) |
R100C |
unknown |
Het |
| Gm7535 |
T |
C |
17: 18,132,061 (GRCm39) |
|
probably benign |
Het |
| Gxylt2 |
T |
G |
6: 100,764,179 (GRCm39) |
L288R |
probably damaging |
Het |
| Mgat4c |
T |
A |
10: 102,225,140 (GRCm39) |
F451L |
possibly damaging |
Het |
| Mrpl20 |
G |
A |
4: 155,888,162 (GRCm39) |
R17H |
probably damaging |
Het |
| Mtf2 |
A |
G |
5: 108,252,365 (GRCm39) |
T465A |
possibly damaging |
Het |
| Mycbp2 |
A |
C |
14: 103,583,757 (GRCm39) |
L66R |
probably benign |
Het |
| Nos1ap |
T |
A |
1: 170,176,968 (GRCm39) |
K145M |
probably damaging |
Het |
| Nr2e1 |
A |
T |
10: 42,447,483 (GRCm39) |
Y176* |
probably null |
Het |
| Obscn |
T |
C |
11: 58,903,541 (GRCm39) |
T7628A |
possibly damaging |
Het |
| Or7a37 |
A |
T |
10: 78,806,390 (GRCm39) |
K302N |
possibly damaging |
Het |
| Pitx2 |
T |
G |
3: 129,009,489 (GRCm39) |
V129G |
probably damaging |
Het |
| Polr2e |
A |
G |
10: 79,873,897 (GRCm39) |
|
probably benign |
Het |
| Ppard |
A |
G |
17: 28,517,832 (GRCm39) |
D300G |
probably damaging |
Het |
| Ppp1r27 |
A |
G |
11: 120,441,743 (GRCm39) |
V46A |
probably benign |
Het |
| Prex2 |
T |
A |
1: 11,177,902 (GRCm39) |
V332E |
probably damaging |
Het |
| Prss30 |
T |
G |
17: 24,191,750 (GRCm39) |
Y257S |
probably benign |
Het |
| Ptprd |
T |
C |
4: 75,900,863 (GRCm39) |
E1082G |
probably damaging |
Het |
| Rab3c |
T |
A |
13: 110,317,611 (GRCm39) |
R89S |
probably damaging |
Het |
| Rimbp2 |
A |
G |
5: 128,874,445 (GRCm39) |
V389A |
possibly damaging |
Het |
| Rims1 |
T |
A |
1: 22,635,623 (GRCm39) |
R119S |
probably damaging |
Het |
| Sema3b |
T |
C |
9: 107,480,536 (GRCm39) |
H137R |
probably null |
Het |
| Sf3b4 |
G |
C |
3: 96,080,958 (GRCm39) |
A89P |
probably damaging |
Het |
| Sgta |
T |
A |
10: 80,882,081 (GRCm39) |
Q298L |
probably damaging |
Het |
| Skic3 |
G |
A |
13: 76,295,886 (GRCm39) |
E1050K |
possibly damaging |
Het |
| Spag9 |
C |
A |
11: 93,959,838 (GRCm39) |
D342E |
probably damaging |
Het |
| Sry |
T |
A |
Y: 2,662,982 (GRCm39) |
D226V |
unknown |
Het |
| Sv2a |
A |
G |
3: 96,092,774 (GRCm39) |
E158G |
possibly damaging |
Het |
| Sytl2 |
A |
G |
7: 90,031,071 (GRCm39) |
|
probably benign |
Het |
| Thbs3 |
T |
A |
3: 89,125,283 (GRCm39) |
|
probably benign |
Het |
| Top3a |
A |
T |
11: 60,653,365 (GRCm39) |
N56K |
possibly damaging |
Het |
| Tyk2 |
T |
C |
9: 21,020,677 (GRCm39) |
D918G |
probably damaging |
Het |
| Uqcrh |
A |
G |
4: 115,924,481 (GRCm39) |
|
probably benign |
Het |
| Vmn1r61 |
A |
G |
7: 5,613,814 (GRCm39) |
S167P |
probably damaging |
Het |
| Wdr25 |
C |
A |
12: 108,992,366 (GRCm39) |
H74N |
probably damaging |
Het |
| Zfp458 |
T |
C |
13: 67,404,382 (GRCm39) |
N686D |
probably benign |
Het |
| Zfp574 |
T |
A |
7: 24,780,515 (GRCm39) |
H512Q |
|
Het |
| Zfp976 |
A |
T |
7: 42,262,902 (GRCm39) |
Y312N |
probably benign |
Het |
| Zscan4c |
G |
A |
7: 10,743,462 (GRCm39) |
V354I |
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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TCCTGAGATGAAGTGGAGCC -3'
(R):5'- GGGACTTGCGTTTAAGACTCC -3'
Sequencing Primer
(F):5'- CCCAGGCTGGAAGATGATTTC -3'
(R):5'- CTTGCGTTTAAGACTCCTGAAAATG -3'
|
| Posted On |
2016-07-22 |
Incidental Mutation