Incidental Mutation 'IGL01609:Kdm4d'
| ID |
91902 |
| 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 # |
IGL01609
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
9 |
| Chromosomal Location |
14373844-14411778 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 14375714 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 48
(V48A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000061632
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000058796]
[ENSMUST00000115647]
|
| AlphaFold |
Q3U2K5 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000058796
AA Change: V48A
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: V48A
| 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: V48A
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914
AA Change: V48A
| 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: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ablim3 |
A |
G |
18: 61,955,092 (GRCm39) |
V299A |
probably benign |
Het |
| Actr5 |
T |
C |
2: 158,478,722 (GRCm39) |
|
probably null |
Het |
| Arhgap18 |
A |
G |
10: 26,756,744 (GRCm39) |
D448G |
possibly damaging |
Het |
| Bcl9 |
T |
C |
3: 97,116,291 (GRCm39) |
E801G |
probably benign |
Het |
| Bin1 |
A |
G |
18: 32,552,978 (GRCm39) |
N232S |
probably damaging |
Het |
| Brf1 |
A |
C |
12: 112,927,211 (GRCm39) |
Y459D |
probably damaging |
Het |
| Clca4a |
T |
A |
3: 144,659,541 (GRCm39) |
I772F |
probably damaging |
Het |
| Cyp2a4 |
G |
A |
7: 26,008,088 (GRCm39) |
|
probably null |
Het |
| Dync1i2 |
T |
A |
2: 71,077,352 (GRCm39) |
|
probably benign |
Het |
| Frem3 |
T |
A |
8: 81,339,333 (GRCm39) |
M542K |
probably benign |
Het |
| Gpbp1 |
T |
C |
13: 111,575,736 (GRCm39) |
T256A |
possibly damaging |
Het |
| Ighm |
T |
C |
12: 113,384,854 (GRCm39) |
|
probably benign |
Het |
| Igkv3-12 |
A |
G |
6: 70,495,232 (GRCm39) |
|
probably benign |
Het |
| Lama2 |
T |
C |
10: 27,220,417 (GRCm39) |
S483G |
probably benign |
Het |
| Lbp |
A |
C |
2: 158,170,332 (GRCm39) |
Q464P |
probably damaging |
Het |
| Lipo4 |
T |
C |
19: 33,476,654 (GRCm39) |
T365A |
probably benign |
Het |
| Mark3 |
T |
C |
12: 111,593,956 (GRCm39) |
F274S |
probably damaging |
Het |
| Mcm3 |
A |
T |
1: 20,884,904 (GRCm39) |
|
probably benign |
Het |
| Mrpl9 |
T |
A |
3: 94,352,001 (GRCm39) |
F137I |
probably damaging |
Het |
| Msh4 |
G |
T |
3: 153,603,034 (GRCm39) |
A93E |
probably damaging |
Het |
| Mthfd1l |
T |
A |
10: 3,968,567 (GRCm39) |
D407E |
probably benign |
Het |
| Or10j7 |
G |
A |
1: 173,011,843 (GRCm39) |
H53Y |
probably benign |
Het |
| Or12d12 |
C |
T |
17: 37,610,629 (GRCm39) |
R228H |
probably benign |
Het |
| Or1i2 |
A |
C |
10: 78,447,960 (GRCm39) |
S172A |
probably benign |
Het |
| Pcsk2 |
G |
T |
2: 143,643,078 (GRCm39) |
V452L |
possibly damaging |
Het |
| Pcsk6 |
G |
A |
7: 65,685,021 (GRCm39) |
|
probably null |
Het |
| Pmfbp1 |
A |
G |
8: 110,254,348 (GRCm39) |
E461G |
probably benign |
Het |
| Pole2 |
A |
G |
12: 69,254,631 (GRCm39) |
|
probably null |
Het |
| Postn |
T |
C |
3: 54,276,649 (GRCm39) |
M176T |
probably damaging |
Het |
| Prss12 |
T |
A |
3: 123,276,483 (GRCm39) |
C371S |
probably damaging |
Het |
| Rnf11 |
T |
A |
4: 109,314,173 (GRCm39) |
Q72L |
possibly damaging |
Het |
| Rrad |
A |
G |
8: 105,356,456 (GRCm39) |
|
probably null |
Het |
| Slitrk3 |
T |
A |
3: 72,957,570 (GRCm39) |
I401F |
probably damaging |
Het |
| Themis |
A |
G |
10: 28,544,749 (GRCm39) |
|
probably benign |
Het |
| Tmem45a |
A |
G |
16: 56,631,928 (GRCm39) |
I230T |
probably benign |
Het |
| Tnni1 |
C |
A |
1: 135,733,234 (GRCm39) |
|
probably null |
Het |
| Trpa1 |
A |
T |
1: 14,982,607 (GRCm39) |
I83N |
probably damaging |
Het |
| Uggt1 |
T |
C |
1: 36,221,555 (GRCm39) |
Y54C |
probably damaging |
Het |
| Umodl1 |
C |
T |
17: 31,217,800 (GRCm39) |
T1202I |
possibly damaging |
Het |
| Unc93a2 |
A |
G |
17: 7,637,138 (GRCm39) |
V130A |
probably damaging |
Het |
| Usp37 |
G |
A |
1: 74,514,199 (GRCm39) |
A324V |
probably benign |
Het |
| Zfp808 |
T |
A |
13: 62,321,023 (GRCm39) |
C751S |
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 |
|
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 |
|
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 |
2013-12-09 |
Incidental Mutation