Incidental Mutation 'R0551:Kdm4a'
| ID |
45154 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4a
|
| Ensembl Gene |
ENSMUSG00000033326 |
| Gene Name |
lysine (K)-specific demethylase 4A |
| Synonyms |
D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2 |
| MMRRC Submission |
038743-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.643)
|
| Stock # |
R0551 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
117994154-118037240 bp(-) (GRCm39) |
| Type of Mutation |
makesense |
| DNA Base Change (assembly) |
T to C
at 117995428 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Stop codon to Tryptophan
at position 1065
(*1065W)
|
| 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 null
Transcript: ENSMUST00000097911
AA Change: *1065W
|
| SMART Domains |
Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: *1065W
| 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 null
Transcript: ENSMUST00000106403
AA Change: *1065W
|
| SMART Domains |
Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: *1065W
| 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 null
Transcript: ENSMUST00000106406
AA Change: *1065W
|
| SMART Domains |
Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: *1065W
| 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 |
0.9566 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.1%
- 20x: 95.1%
|
| Validation Efficiency |
99% (77/78) |
| 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: 75 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 3425401B19Rik |
T |
A |
14: 32,384,598 (GRCm39) |
T456S |
probably benign |
Het |
| Acmsd |
A |
T |
1: 127,694,070 (GRCm39) |
K333N |
probably benign |
Het |
| Adcy2 |
T |
A |
13: 68,944,658 (GRCm39) |
K241N |
probably damaging |
Het |
| Aebp1 |
A |
G |
11: 5,817,955 (GRCm39) |
I77V |
probably benign |
Het |
| Albfm1 |
C |
T |
5: 90,720,578 (GRCm39) |
P250S |
probably damaging |
Het |
| Ankrd35 |
A |
G |
3: 96,591,276 (GRCm39) |
T521A |
probably benign |
Het |
| Arap2 |
C |
T |
5: 62,798,666 (GRCm39) |
|
probably null |
Het |
| Arfgap3 |
A |
T |
15: 83,227,338 (GRCm39) |
C25S |
probably damaging |
Het |
| Arhgap20 |
T |
A |
9: 51,737,125 (GRCm39) |
|
probably benign |
Het |
| Arhgap39 |
C |
T |
15: 76,619,086 (GRCm39) |
D833N |
probably damaging |
Het |
| Auts2 |
T |
C |
5: 131,469,307 (GRCm39) |
E446G |
possibly damaging |
Het |
| Brwd1 |
C |
T |
16: 95,837,174 (GRCm39) |
R886H |
probably damaging |
Het |
| Carm1 |
G |
A |
9: 21,491,787 (GRCm39) |
|
probably null |
Het |
| Cdc5l |
G |
A |
17: 45,726,610 (GRCm39) |
R321W |
probably damaging |
Het |
| Cfap54 |
A |
T |
10: 92,860,984 (GRCm39) |
M841K |
probably benign |
Het |
| Clca4b |
T |
A |
3: 144,634,387 (GRCm39) |
T69S |
probably damaging |
Het |
| Cpox |
A |
G |
16: 58,495,753 (GRCm39) |
I357V |
probably benign |
Het |
| Diaph3 |
C |
A |
14: 87,147,536 (GRCm39) |
V711L |
probably benign |
Het |
| Fabp3-ps1 |
T |
C |
10: 86,567,904 (GRCm39) |
|
probably benign |
Het |
| Fam120b |
A |
T |
17: 15,651,905 (GRCm39) |
|
probably benign |
Het |
| Fcho1 |
A |
G |
8: 72,164,818 (GRCm39) |
S488P |
probably benign |
Het |
| Flcn |
A |
G |
11: 59,686,574 (GRCm39) |
|
probably null |
Het |
| Flt3l |
A |
G |
7: 44,781,690 (GRCm39) |
W234R |
probably damaging |
Het |
| Fzd7 |
G |
T |
1: 59,522,443 (GRCm39) |
V109L |
probably damaging |
Het |
| G3bp1 |
A |
G |
11: 55,379,969 (GRCm39) |
N101S |
probably benign |
Het |
| Gadd45g |
A |
G |
13: 52,001,963 (GRCm39) |
E143G |
probably damaging |
Het |
| Ganab |
T |
G |
19: 8,884,644 (GRCm39) |
I149S |
probably benign |
Het |
| Garnl3 |
A |
G |
2: 32,906,750 (GRCm39) |
S413P |
probably damaging |
Het |
| Glis1 |
C |
T |
4: 107,425,316 (GRCm39) |
|
probably null |
Het |
| Gm11563 |
A |
G |
11: 99,549,539 (GRCm39) |
S72P |
unknown |
Het |
| Gpd1 |
T |
G |
15: 99,618,510 (GRCm39) |
I188S |
possibly damaging |
Het |
| Gria2 |
A |
G |
3: 80,639,333 (GRCm39) |
|
probably benign |
Het |
| Hpcal4 |
G |
T |
4: 123,082,848 (GRCm39) |
A65S |
possibly damaging |
Het |
| Igsf10 |
G |
A |
3: 59,236,089 (GRCm39) |
T1364I |
probably benign |
Het |
| Klkb1 |
A |
G |
8: 45,731,003 (GRCm39) |
|
probably null |
Het |
| Lipo3 |
T |
C |
19: 33,557,951 (GRCm39) |
D147G |
probably damaging |
Het |
| Lrp1 |
A |
G |
10: 127,407,827 (GRCm39) |
S1821P |
probably benign |
Het |
| Macroh2a2 |
A |
G |
10: 61,576,945 (GRCm39) |
S308P |
probably damaging |
Het |
| Manba |
T |
C |
3: 135,223,734 (GRCm39) |
I207T |
probably damaging |
Het |
| Mark3 |
T |
A |
12: 111,600,068 (GRCm39) |
S428T |
probably benign |
Het |
| Mfsd4a |
G |
A |
1: 131,969,657 (GRCm39) |
T348I |
probably damaging |
Het |
| Mybbp1a |
A |
G |
11: 72,339,202 (GRCm39) |
M880V |
probably benign |
Het |
| N4bp2 |
T |
A |
5: 65,977,684 (GRCm39) |
|
probably null |
Het |
| Nrdc |
T |
G |
4: 108,904,905 (GRCm39) |
I712S |
probably damaging |
Het |
| Nup210 |
G |
A |
6: 90,998,466 (GRCm39) |
R774C |
possibly damaging |
Het |
| Obscn |
G |
A |
11: 58,998,688 (GRCm39) |
R1395* |
probably null |
Het |
| Or5b102 |
T |
A |
19: 13,041,658 (GRCm39) |
D294E |
probably benign |
Het |
| Pcdh7 |
T |
C |
5: 57,879,336 (GRCm39) |
Y964H |
probably damaging |
Het |
| Pgap6 |
C |
A |
17: 26,339,576 (GRCm39) |
Q605K |
probably damaging |
Het |
| Plin4 |
T |
C |
17: 56,413,756 (GRCm39) |
T290A |
probably benign |
Het |
| Ppara |
T |
C |
15: 85,671,306 (GRCm39) |
|
probably benign |
Het |
| Psg21 |
T |
G |
7: 18,386,565 (GRCm39) |
|
probably null |
Het |
| Ptar1 |
C |
A |
19: 23,697,704 (GRCm39) |
N405K |
probably benign |
Het |
| Ralgps2 |
A |
G |
1: 156,660,233 (GRCm39) |
|
probably null |
Het |
| Rnf6 |
T |
A |
5: 146,148,205 (GRCm39) |
N271I |
possibly damaging |
Het |
| Sis |
T |
C |
3: 72,832,740 (GRCm39) |
D1019G |
possibly damaging |
Het |
| Slc37a3 |
A |
G |
6: 39,329,688 (GRCm39) |
|
probably benign |
Het |
| Slc49a3 |
A |
G |
5: 108,592,331 (GRCm39) |
|
probably benign |
Het |
| Slc6a12 |
G |
A |
6: 121,333,877 (GRCm39) |
V238I |
probably damaging |
Het |
| Sntg1 |
C |
A |
1: 8,624,960 (GRCm39) |
V279L |
possibly damaging |
Het |
| Sorbs1 |
T |
A |
19: 40,300,260 (GRCm39) |
E567D |
probably damaging |
Het |
| Sp110 |
C |
A |
1: 85,516,821 (GRCm39) |
|
probably benign |
Het |
| Ssu2 |
A |
G |
6: 112,357,515 (GRCm39) |
V175A |
possibly damaging |
Het |
| Stk36 |
G |
A |
1: 74,655,780 (GRCm39) |
E428K |
probably benign |
Het |
| Teddm1b |
A |
T |
1: 153,751,090 (GRCm39) |
I300F |
possibly damaging |
Het |
| Thy1 |
T |
C |
9: 43,958,645 (GRCm39) |
V129A |
probably damaging |
Het |
| Tiam2 |
T |
A |
17: 3,479,229 (GRCm39) |
M654K |
probably damaging |
Het |
| Tmem69 |
T |
C |
4: 116,410,470 (GRCm39) |
S167G |
probably benign |
Het |
| Tmem81 |
C |
G |
1: 132,435,567 (GRCm39) |
I124M |
probably damaging |
Het |
| Tspan10 |
A |
G |
11: 120,335,244 (GRCm39) |
D118G |
probably damaging |
Het |
| Tspo2 |
A |
G |
17: 48,755,841 (GRCm39) |
|
probably benign |
Het |
| Ttn |
G |
A |
2: 76,738,672 (GRCm39) |
Q4002* |
probably null |
Het |
| Tyro3 |
G |
A |
2: 119,647,385 (GRCm39) |
R834Q |
probably damaging |
Het |
| Ugt2b1 |
T |
C |
5: 87,073,943 (GRCm39) |
K139E |
probably benign |
Het |
| Vmn1r9 |
A |
T |
6: 57,048,524 (GRCm39) |
I200F |
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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TGCAATCACAGCATCCCAGTGTC -3'
(R):5'- TTCTGTGCCCTGAGCATGTGTC -3'
Sequencing Primer
(F):5'- TTCCCGGCAGAATGCATC -3'
(R):5'- CATGTGTCCTGAACATGGCAG -3'
|
| Posted On |
2013-06-11 |
Incidental Mutation