Incidental Mutation 'R0603:Kdm4a'
ID |
55539 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm4a
|
Ensembl Gene |
ENSMUSG00000033326 |
Gene Name |
lysine (K)-specific demethylase 4A |
Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
MMRRC Submission |
038792-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.643)
|
Stock # |
R0603 (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 117999708 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Isoleucine
at position 905
(V905I)
|
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: V905I
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000062910 Gene: ENSMUSG00000033326 AA Change: V905I
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: V905I
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000095524 Gene: ENSMUSG00000033326 AA Change: V905I
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: V905I
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000102011 Gene: ENSMUSG00000033326 AA Change: V905I
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: V905I
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000102014 Gene: ENSMUSG00000033326 AA Change: V905I
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: ENSMUST00000152808
|
Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.9%
- 10x: 97.6%
- 20x: 95.3%
|
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: 52 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Anapc7 |
A |
G |
5: 122,578,233 (GRCm39) |
N406S |
probably benign |
Het |
Arhgap4 |
C |
T |
X: 72,950,389 (GRCm39) |
R54Q |
probably damaging |
Het |
Asb15 |
T |
A |
6: 24,556,556 (GRCm39) |
I17N |
probably damaging |
Het |
Atp8a1 |
T |
C |
5: 67,914,039 (GRCm39) |
|
probably null |
Het |
Caprin1 |
A |
G |
2: 103,627,146 (GRCm39) |
V47A |
probably benign |
Het |
Col4a2 |
T |
C |
8: 11,464,779 (GRCm39) |
V348A |
probably benign |
Het |
Disp2 |
A |
G |
2: 118,622,487 (GRCm39) |
K1073R |
probably damaging |
Het |
Dmxl2 |
G |
A |
9: 54,313,190 (GRCm39) |
H1686Y |
possibly damaging |
Het |
Dzank1 |
C |
T |
2: 144,353,432 (GRCm39) |
V152I |
probably benign |
Het |
Elp1 |
A |
T |
4: 56,792,105 (GRCm39) |
I221N |
possibly damaging |
Het |
Evl |
T |
A |
12: 108,614,681 (GRCm39) |
I25N |
probably damaging |
Het |
Fam117a |
A |
G |
11: 95,271,699 (GRCm39) |
K424E |
probably damaging |
Het |
Gm17732 |
C |
T |
18: 62,795,823 (GRCm39) |
|
probably benign |
Het |
Gpr158 |
T |
C |
2: 21,820,480 (GRCm39) |
I659T |
possibly damaging |
Het |
Hectd4 |
T |
A |
5: 121,442,400 (GRCm39) |
V1280E |
possibly damaging |
Het |
Irs4 |
T |
C |
X: 140,508,071 (GRCm39) |
T42A |
probably damaging |
Het |
Lmtk3 |
T |
A |
7: 45,444,980 (GRCm39) |
|
probably benign |
Het |
Lsp1 |
G |
A |
7: 142,043,115 (GRCm39) |
R221H |
probably damaging |
Het |
Marf1 |
C |
T |
16: 13,960,398 (GRCm39) |
A549T |
probably damaging |
Het |
Mmut |
A |
T |
17: 41,258,057 (GRCm39) |
I408F |
probably damaging |
Het |
Nckap1 |
A |
T |
2: 80,343,073 (GRCm39) |
V942E |
probably benign |
Het |
Neto1 |
T |
A |
18: 86,491,785 (GRCm39) |
C229S |
possibly damaging |
Het |
Nipal2 |
A |
G |
15: 34,650,544 (GRCm39) |
I63T |
probably damaging |
Het |
Or11g2 |
T |
C |
14: 50,855,967 (GRCm39) |
I96T |
probably damaging |
Het |
Or1af1 |
G |
A |
2: 37,110,118 (GRCm39) |
V206I |
probably damaging |
Het |
Or4k49 |
A |
T |
2: 111,495,225 (GRCm39) |
Y218F |
probably damaging |
Het |
Or7e165 |
A |
T |
9: 19,695,235 (GRCm39) |
R269W |
probably damaging |
Het |
Or8g36 |
C |
A |
9: 39,422,810 (GRCm39) |
V69F |
possibly damaging |
Het |
Pgpep1 |
T |
C |
8: 71,103,283 (GRCm39) |
E120G |
probably benign |
Het |
Pkhd1 |
A |
T |
1: 20,187,397 (GRCm39) |
M3637K |
probably benign |
Het |
Pkm |
T |
C |
9: 59,573,164 (GRCm39) |
V58A |
probably damaging |
Het |
Ppp2r1b |
C |
A |
9: 50,772,985 (GRCm39) |
T154K |
probably damaging |
Het |
Rgs18 |
T |
A |
1: 144,631,818 (GRCm39) |
D98V |
possibly damaging |
Het |
Rsph6a |
G |
T |
7: 18,799,886 (GRCm39) |
A506S |
possibly damaging |
Het |
Selenop |
T |
A |
15: 3,305,183 (GRCm39) |
V113E |
probably damaging |
Het |
Slc6a11 |
G |
A |
6: 114,221,851 (GRCm39) |
V514M |
probably benign |
Het |
Srsf9 |
C |
T |
5: 115,470,696 (GRCm39) |
S132L |
probably damaging |
Het |
Tchh |
G |
A |
3: 93,351,088 (GRCm39) |
R176H |
possibly damaging |
Het |
Tcp11 |
T |
C |
17: 28,286,784 (GRCm39) |
N405S |
probably damaging |
Het |
Tle1 |
A |
C |
4: 72,036,584 (GRCm39) |
D760E |
probably damaging |
Het |
Tmem178 |
A |
G |
17: 81,252,488 (GRCm39) |
D124G |
possibly damaging |
Het |
Trabd |
G |
A |
15: 88,966,929 (GRCm39) |
E118K |
probably damaging |
Het |
Ttc39a |
A |
G |
4: 109,283,499 (GRCm39) |
D115G |
probably damaging |
Het |
Uaca |
T |
A |
9: 60,778,379 (GRCm39) |
M920K |
possibly damaging |
Het |
Uba2 |
A |
T |
7: 33,861,038 (GRCm39) |
M5K |
probably damaging |
Het |
Unc5c |
C |
T |
3: 141,476,863 (GRCm39) |
P343L |
probably damaging |
Het |
Wdhd1 |
T |
C |
14: 47,501,043 (GRCm39) |
D453G |
probably damaging |
Het |
Wfdc8 |
A |
G |
2: 164,445,145 (GRCm39) |
Y157H |
probably damaging |
Het |
Zbbx |
T |
G |
3: 74,985,757 (GRCm39) |
K432Q |
probably benign |
Het |
Zeb2 |
G |
A |
2: 44,907,438 (GRCm39) |
T169M |
probably benign |
Het |
Zfp956 |
A |
G |
6: 47,932,962 (GRCm39) |
E79G |
probably damaging |
Het |
Zzef1 |
G |
A |
11: 72,708,895 (GRCm39) |
V165I |
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 |
|
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 |
|
|
Predicted Primers |
PCR Primer
(F):5'- CCAGAAGCCGCTTTCAGACATTACC -3'
(R):5'- ATAGGCTGAGGCAGGACATTGCTG -3'
Sequencing Primer
(F):5'- CCACTATGTCCTCAGGATAAAGGTTG -3'
(R):5'- GCAGGACATTGCTGTAAATTGG -3'
|
Posted On |
2013-07-11 |