Incidental Mutation 'IGL03379:Kdm4d'
| ID |
420629 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Kdm4d
|
| Ensembl Gene |
ENSMUSG00000053914 |
| Gene Name |
lysine (K)-specific demethylase 4D |
| Synonyms |
Jmjd2d |
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
IGL03379
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
9 |
| Chromosomal Location |
14373844-14411778 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 14375139 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Glycine
at position 240
(R240G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000111311
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000058796]
[ENSMUST00000115647]
|
| AlphaFold |
Q3U2K5 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000058796
AA Change: R240G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: R240G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:JmjN
|
16 |
50 |
3.3e-15 |
PFAM |
|
JmjC
|
143 |
309 |
2.3e-57 |
SMART |
|
low complexity region
|
370 |
383 |
N/A |
INTRINSIC |
|
low complexity region
|
417 |
434 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000115647
AA Change: R240G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914
AA Change: R240G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:JmjN
|
16 |
50 |
1.1e-16 |
PFAM |
|
JmjC
|
143 |
309 |
2.3e-57 |
SMART |
|
low complexity region
|
370 |
383 |
N/A |
INTRINSIC |
|
low complexity region
|
417 |
434 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| MGI Phenotype |
PHENOTYPE: Mice homozygous for a knock-out allele exhibit accumulation of histone 3 methylation in spermatids, a transient increase in testes size, wider tubules, occasional male germ cell apoptosis, and decreased body weight. However, fertility is normal. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 39 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ank3 |
A |
G |
10: 69,809,602 (GRCm39) |
T260A |
probably damaging |
Het |
| Arhgap21 |
A |
G |
2: 20,885,500 (GRCm39) |
V559A |
probably benign |
Het |
| Arrdc5 |
G |
A |
17: 56,601,589 (GRCm39) |
Q179* |
probably null |
Het |
| Atrnl1 |
T |
C |
19: 57,630,973 (GRCm39) |
Y247H |
probably benign |
Het |
| Bend5 |
T |
A |
4: 111,311,468 (GRCm39) |
S361T |
probably benign |
Het |
| Cdc20b |
A |
G |
13: 113,217,736 (GRCm39) |
D385G |
probably damaging |
Het |
| Cep120 |
C |
T |
18: 53,842,208 (GRCm39) |
S709N |
probably benign |
Het |
| Eif2b4 |
A |
G |
5: 31,347,355 (GRCm39) |
|
probably benign |
Het |
| Eif2s1 |
T |
A |
12: 78,913,354 (GRCm39) |
D18E |
probably benign |
Het |
| Etl4 |
G |
A |
2: 20,666,827 (GRCm39) |
S209N |
possibly damaging |
Het |
| Farp2 |
T |
A |
1: 93,535,160 (GRCm39) |
F636L |
probably benign |
Het |
| Fcgbp |
A |
T |
7: 27,789,342 (GRCm39) |
D636V |
possibly damaging |
Het |
| Gm5082 |
T |
C |
13: 41,809,902 (GRCm39) |
|
noncoding transcript |
Het |
| Gtf2ird1 |
C |
T |
5: 134,411,392 (GRCm39) |
G672D |
possibly damaging |
Het |
| Heatr3 |
A |
G |
8: 88,876,738 (GRCm39) |
K143R |
probably benign |
Het |
| Hrc |
A |
G |
7: 44,986,679 (GRCm39) |
E610G |
probably benign |
Het |
| Ica1l |
G |
A |
1: 60,036,780 (GRCm39) |
S337F |
probably benign |
Het |
| Ighv1-43 |
T |
C |
12: 114,909,625 (GRCm39) |
Y99C |
probably benign |
Het |
| Kcna3 |
T |
A |
3: 106,944,521 (GRCm39) |
F261L |
probably benign |
Het |
| Kidins220 |
T |
A |
12: 25,058,447 (GRCm39) |
I620N |
probably damaging |
Het |
| Kif5c |
A |
G |
2: 49,591,104 (GRCm39) |
M55V |
probably damaging |
Het |
| Oas1a |
A |
T |
5: 121,035,062 (GRCm39) |
L366Q |
possibly damaging |
Het |
| Or5p68 |
T |
C |
7: 107,946,196 (GRCm39) |
|
probably benign |
Het |
| Pds5b |
T |
C |
5: 150,711,796 (GRCm39) |
V918A |
probably damaging |
Het |
| Plcz1 |
G |
A |
6: 139,936,490 (GRCm39) |
L580F |
possibly damaging |
Het |
| Prlr |
C |
A |
15: 10,319,403 (GRCm39) |
P147T |
possibly damaging |
Het |
| Ptpn18 |
A |
T |
1: 34,509,338 (GRCm39) |
|
probably null |
Het |
| Ptprt |
A |
T |
2: 161,397,379 (GRCm39) |
C1109* |
probably null |
Het |
| Ralgapa2 |
A |
T |
2: 146,199,907 (GRCm39) |
S1212R |
probably benign |
Het |
| Scn2b |
T |
A |
9: 45,037,498 (GRCm39) |
C182S |
probably damaging |
Het |
| Slc7a14 |
A |
T |
3: 31,277,664 (GRCm39) |
M647K |
probably damaging |
Het |
| Sult2a6 |
G |
A |
7: 13,956,511 (GRCm39) |
T250I |
probably benign |
Het |
| Syn3 |
A |
T |
10: 85,900,736 (GRCm39) |
M384K |
possibly damaging |
Het |
| Tmem8b |
A |
G |
4: 43,685,561 (GRCm39) |
T596A |
probably benign |
Het |
| Tnpo1 |
C |
T |
13: 99,000,348 (GRCm39) |
E340K |
probably damaging |
Het |
| Vat1l |
A |
T |
8: 115,009,006 (GRCm39) |
I247F |
probably damaging |
Het |
| Vmn2r110 |
T |
C |
17: 20,803,906 (GRCm39) |
D223G |
probably damaging |
Het |
| Wdr11 |
T |
A |
7: 129,200,847 (GRCm39) |
D99E |
probably damaging |
Het |
| Zan |
C |
T |
5: 137,462,477 (GRCm39) |
V901I |
unknown |
Het |
|
| Other mutations in Kdm4d |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01011:Kdm4d
|
APN |
9 |
14,375,515 (GRCm39) |
missense |
probably benign |
0.10 |
|
IGL01114:Kdm4d
|
APN |
9 |
14,375,493 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01609:Kdm4d
|
APN |
9 |
14,375,714 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02342:Kdm4d
|
APN |
9 |
14,374,860 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02513:Kdm4d
|
APN |
9 |
14,375,850 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03276:Kdm4d
|
APN |
9 |
14,375,838 (GRCm39) |
missense |
probably benign |
0.04 |
|
R0220:Kdm4d
|
UTSW |
9 |
14,374,418 (GRCm39) |
missense |
probably benign |
|
|
R0755:Kdm4d
|
UTSW |
9 |
14,375,591 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1195:Kdm4d
|
UTSW |
9 |
14,374,395 (GRCm39) |
missense |
probably benign |
|
|
R1195:Kdm4d
|
UTSW |
9 |
14,374,395 (GRCm39) |
missense |
probably benign |
|
|
R1195:Kdm4d
|
UTSW |
9 |
14,374,395 (GRCm39) |
missense |
probably benign |
|
|
R1455:Kdm4d
|
UTSW |
9 |
14,375,691 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1552:Kdm4d
|
UTSW |
9 |
14,375,325 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1692:Kdm4d
|
UTSW |
9 |
14,375,807 (GRCm39) |
missense |
probably benign |
0.43 |
|
R1871:Kdm4d
|
UTSW |
9 |
14,375,679 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1892:Kdm4d
|
UTSW |
9 |
14,375,613 (GRCm39) |
missense |
probably benign |
0.14 |
|
R4792:Kdm4d
|
UTSW |
9 |
14,374,686 (GRCm39) |
missense |
probably benign |
|
|
R5113:Kdm4d
|
UTSW |
9 |
14,375,409 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5211:Kdm4d
|
UTSW |
9 |
14,374,400 (GRCm39) |
missense |
probably benign |
0.04 |
|
R5352:Kdm4d
|
UTSW |
9 |
14,375,654 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6692:Kdm4d
|
UTSW |
9 |
14,374,361 (GRCm39) |
missense |
probably benign |
|
|
R7014:Kdm4d
|
UTSW |
9 |
14,375,475 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7198:Kdm4d
|
UTSW |
9 |
14,375,316 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7260:Kdm4d
|
UTSW |
9 |
14,374,454 (GRCm39) |
missense |
probably benign |
0.05 |
|
R8116:Kdm4d
|
UTSW |
9 |
14,375,237 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8134:Kdm4d
|
UTSW |
9 |
14,374,532 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8354:Kdm4d
|
UTSW |
9 |
14,375,235 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R9006:Kdm4d
|
UTSW |
9 |
14,374,833 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9197:Kdm4d
|
UTSW |
9 |
14,375,537 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9298:Kdm4d
|
UTSW |
9 |
14,375,336 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9300:Kdm4d
|
UTSW |
9 |
14,375,336 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Posted On |
2016-08-02 |
Incidental Mutation