Incidental Mutation 'R6692:Kdm4d'
| ID |
527917 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm4d
|
| Ensembl Gene |
ENSMUSG00000053914 |
| Gene Name |
lysine (K)-specific demethylase 4D |
| Synonyms |
Jmjd2d |
| MMRRC Submission |
044810-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6692 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
14373844-14411778 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 14374361 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Lysine
at position 499
(M499K)
|
| 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: M499K
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: M499K
| 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
|
| SMART Domains |
Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914
| 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 |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.0%
- 20x: 94.1%
|
| Validation Efficiency |
100% (38/38) |
| 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: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ahcyl1 |
C |
T |
3: 107,582,401 (GRCm39) |
G54D |
probably damaging |
Het |
| Aldh1b1 |
T |
C |
4: 45,803,427 (GRCm39) |
C322R |
probably damaging |
Het |
| Cdc14b |
T |
C |
13: 64,363,377 (GRCm39) |
I258V |
probably damaging |
Het |
| Cenph |
T |
C |
13: 100,909,243 (GRCm39) |
I55V |
probably benign |
Het |
| Cep290 |
T |
A |
10: 100,405,006 (GRCm39) |
|
probably null |
Het |
| Ces2b |
A |
G |
8: 105,563,919 (GRCm39) |
Y431C |
probably damaging |
Het |
| Cyp4f17 |
T |
C |
17: 32,725,950 (GRCm39) |
S28P |
possibly damaging |
Het |
| Cyp4f40 |
C |
G |
17: 32,894,716 (GRCm39) |
T427S |
possibly damaging |
Het |
| Exoc2 |
A |
G |
13: 31,119,490 (GRCm39) |
I137T |
probably benign |
Het |
| Fam168b |
C |
A |
1: 34,875,822 (GRCm39) |
G21V |
probably damaging |
Het |
| G3bp1 |
T |
A |
11: 55,384,335 (GRCm39) |
D168E |
probably benign |
Het |
| Impg2 |
T |
A |
16: 56,072,696 (GRCm39) |
L376H |
probably damaging |
Het |
| Lonp1 |
C |
T |
17: 56,926,230 (GRCm39) |
V426M |
probably damaging |
Het |
| Lypla2 |
C |
A |
4: 135,698,173 (GRCm39) |
A26S |
probably benign |
Het |
| Map3k13 |
T |
C |
16: 21,723,987 (GRCm39) |
V323A |
possibly damaging |
Het |
| Mdfic2 |
T |
G |
6: 98,225,169 (GRCm39) |
H38P |
possibly damaging |
Het |
| Mov10 |
A |
G |
3: 104,725,360 (GRCm39) |
L83P |
probably damaging |
Het |
| Mphosph9 |
G |
T |
5: 124,398,179 (GRCm39) |
A1039D |
probably damaging |
Het |
| Nedd1 |
T |
C |
10: 92,534,199 (GRCm39) |
K317R |
possibly damaging |
Het |
| Or10ag55-ps1 |
A |
G |
2: 87,139,336 (GRCm39) |
T68A |
possibly damaging |
Het |
| Pde3a |
T |
A |
6: 141,425,072 (GRCm39) |
S623T |
probably damaging |
Het |
| Pld1 |
T |
A |
3: 28,095,348 (GRCm39) |
M227K |
probably benign |
Het |
| Rell1 |
T |
G |
5: 64,095,210 (GRCm39) |
K85N |
probably damaging |
Het |
| Rhbdf1 |
T |
C |
11: 32,165,652 (GRCm39) |
T93A |
probably damaging |
Het |
| Sccpdh |
T |
A |
1: 179,511,792 (GRCm39) |
M88K |
possibly damaging |
Het |
| Siae |
T |
G |
9: 37,554,095 (GRCm39) |
|
probably null |
Het |
| Slc22a16 |
G |
A |
10: 40,479,901 (GRCm39) |
E637K |
unknown |
Het |
| Stk19 |
C |
T |
17: 35,043,770 (GRCm39) |
G95S |
probably benign |
Het |
| Stpg2 |
G |
A |
3: 139,228,738 (GRCm39) |
|
probably null |
Het |
| Sult2a5 |
T |
A |
7: 13,358,057 (GRCm39) |
F30I |
probably damaging |
Het |
| Svil |
A |
G |
18: 5,082,853 (GRCm39) |
E748G |
probably damaging |
Het |
| Swap70 |
T |
A |
7: 109,869,126 (GRCm39) |
H306Q |
probably benign |
Het |
| Try10 |
G |
A |
6: 41,334,755 (GRCm39) |
G227D |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,726,713 (GRCm39) |
|
probably benign |
Het |
| Ttn |
T |
A |
2: 76,749,436 (GRCm39) |
H3871L |
probably benign |
Het |
| Vmn1r231 |
T |
C |
17: 21,110,745 (GRCm39) |
I57V |
possibly damaging |
Het |
| Vpreb1a |
A |
G |
16: 16,686,666 (GRCm39) |
S75P |
probably damaging |
Het |
| Zkscan5 |
A |
G |
5: 145,157,894 (GRCm39) |
|
probably null |
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 |
|
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 |
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- CAATGCAACCTCAGCTGGAAG -3'
(R):5'- GTCGTCCTTGTGAACTAGGAG -3'
Sequencing Primer
(F):5'- TTATCCAGAGGCTTGCCAAG -3'
(R):5'- CCTTGTGAACTAGGAGCTCAG -3'
|
| Posted On |
2018-07-23 |
Incidental Mutation