Incidental Mutation 'IGL02513:Kdm4d'
| ID |
296632 |
| 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 # |
IGL02513
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
9 |
| Chromosomal Location |
14373844-14411778 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 14375850 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Serine
at position 3
(T3S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000061632
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000058796]
[ENSMUST00000115647]
|
| AlphaFold |
Q3U2K5 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000058796
AA Change: T3S
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: T3S
| 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 benign
Transcript: ENSMUST00000115647
AA Change: T3S
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914
AA Change: T3S
| 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: 31 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Apob |
G |
T |
12: 8,042,979 (GRCm39) |
V787F |
probably benign |
Het |
| Atg14 |
T |
C |
14: 47,786,451 (GRCm39) |
I268V |
probably benign |
Het |
| Atg14 |
T |
A |
14: 47,783,081 (GRCm39) |
|
probably benign |
Het |
| Atm |
A |
T |
9: 53,408,562 (GRCm39) |
|
probably benign |
Het |
| Ccdc9 |
A |
G |
7: 16,018,434 (GRCm39) |
|
probably benign |
Het |
| Cers6 |
T |
C |
2: 68,899,013 (GRCm39) |
F217S |
probably benign |
Het |
| Crebbp |
A |
C |
16: 3,944,469 (GRCm39) |
|
probably null |
Het |
| Csmd1 |
T |
A |
8: 16,049,869 (GRCm39) |
|
probably benign |
Het |
| Dmac2l |
A |
T |
12: 69,787,819 (GRCm39) |
Y85F |
probably benign |
Het |
| Eml1 |
T |
A |
12: 108,496,571 (GRCm39) |
V609E |
probably damaging |
Het |
| Fryl |
A |
G |
5: 73,222,636 (GRCm39) |
S204P |
probably damaging |
Het |
| Gpr152 |
A |
G |
19: 4,192,843 (GRCm39) |
D128G |
probably damaging |
Het |
| Itgal |
T |
A |
7: 126,927,844 (GRCm39) |
V1013D |
possibly damaging |
Het |
| Kctd18 |
A |
G |
1: 58,004,559 (GRCm39) |
Y112H |
probably damaging |
Het |
| Lrp1b |
C |
T |
2: 41,000,765 (GRCm39) |
|
probably null |
Het |
| Mex3c |
T |
A |
18: 73,723,360 (GRCm39) |
D484E |
possibly damaging |
Het |
| Nalf1 |
T |
A |
8: 9,257,930 (GRCm39) |
D406V |
probably benign |
Het |
| Nat14 |
T |
C |
7: 4,927,050 (GRCm39) |
V74A |
possibly damaging |
Het |
| Or2b6 |
A |
G |
13: 21,823,510 (GRCm39) |
F61S |
probably damaging |
Het |
| Pabpc2 |
C |
T |
18: 39,908,193 (GRCm39) |
T486I |
probably benign |
Het |
| Pgm2 |
A |
G |
5: 64,260,289 (GRCm39) |
|
probably benign |
Het |
| Pkn3 |
T |
A |
2: 29,973,149 (GRCm39) |
I353N |
probably damaging |
Het |
| Rbm44 |
T |
A |
1: 91,083,260 (GRCm39) |
S594R |
possibly damaging |
Het |
| Rrbp1 |
C |
T |
2: 143,830,350 (GRCm39) |
A606T |
possibly damaging |
Het |
| Tcof1 |
A |
G |
18: 60,964,850 (GRCm39) |
V623A |
possibly damaging |
Het |
| Tg |
A |
G |
15: 66,577,123 (GRCm39) |
E1482G |
probably benign |
Het |
| Uba1 |
A |
G |
X: 20,541,885 (GRCm39) |
T546A |
probably benign |
Het |
| Vmn2r37 |
T |
C |
7: 9,220,934 (GRCm39) |
K310E |
probably benign |
Het |
| Zbtb38 |
A |
T |
9: 96,569,126 (GRCm39) |
W653R |
probably damaging |
Het |
| Zdhhc19 |
A |
T |
16: 32,318,440 (GRCm39) |
I99F |
probably damaging |
Het |
| Zfp236 |
T |
C |
18: 82,648,239 (GRCm39) |
Y974C |
probably damaging |
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 |
|
IGL03276:Kdm4d
|
APN |
9 |
14,375,838 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL03379:Kdm4d
|
APN |
9 |
14,375,139 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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 |
2015-04-16 |
Incidental Mutation