Incidental Mutation 'R5211:Kdm4d'
ID |
403136 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm4d
|
Ensembl Gene |
ENSMUSG00000053914 |
Gene Name |
lysine (K)-specific demethylase 4D |
Synonyms |
Jmjd2d |
MMRRC Submission |
042785-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R5211 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
9 |
Chromosomal Location |
14373844-14411778 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to C
at 14374400 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Glycine
at position 486
(V486G)
|
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: V486G
PolyPhen 2
Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
|
SMART Domains |
Protein: ENSMUSP00000061632 Gene: ENSMUSG00000053914 AA Change: V486G
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 |
|
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.8%
|
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 |
9930012K11Rik |
A |
G |
14: 70,394,233 (GRCm39) |
S181P |
probably benign |
Het |
Adgrf5 |
A |
T |
17: 43,733,511 (GRCm39) |
T112S |
probably benign |
Het |
Ascc2 |
T |
C |
11: 4,623,399 (GRCm39) |
V545A |
possibly damaging |
Het |
Bmp2 |
A |
T |
2: 133,396,550 (GRCm39) |
S69C |
probably damaging |
Het |
Btaf1 |
T |
A |
19: 36,973,962 (GRCm39) |
I1378K |
probably benign |
Het |
Ces2b |
C |
T |
8: 105,561,695 (GRCm39) |
T263I |
possibly damaging |
Het |
Cntn5 |
A |
T |
9: 9,704,894 (GRCm39) |
V635D |
possibly damaging |
Het |
Dock6 |
T |
C |
9: 21,731,648 (GRCm39) |
E1218G |
probably benign |
Het |
Eml6 |
T |
C |
11: 29,804,145 (GRCm39) |
I319V |
probably benign |
Het |
Esd |
T |
C |
14: 74,978,632 (GRCm39) |
S65P |
probably damaging |
Het |
Exoc1l |
C |
A |
5: 76,664,250 (GRCm39) |
T113K |
possibly damaging |
Het |
Fstl3 |
A |
T |
10: 79,616,012 (GRCm39) |
Q166L |
probably benign |
Het |
Garin1a |
A |
T |
6: 29,286,098 (GRCm39) |
K128* |
probably null |
Het |
Gcn1 |
T |
A |
5: 115,757,371 (GRCm39) |
S2445T |
probably benign |
Het |
Gfy |
C |
A |
7: 44,827,282 (GRCm39) |
L271F |
possibly damaging |
Het |
Gjc2 |
A |
G |
11: 59,068,284 (GRCm39) |
V66A |
possibly damaging |
Het |
H3c4 |
G |
T |
13: 23,760,015 (GRCm39) |
G14C |
possibly damaging |
Het |
Itm2c |
T |
A |
1: 85,834,249 (GRCm39) |
V188E |
probably damaging |
Het |
Jmjd1c |
C |
G |
10: 67,067,795 (GRCm39) |
S1766C |
probably damaging |
Het |
Kcnn3 |
A |
G |
3: 89,428,538 (GRCm39) |
T255A |
probably benign |
Het |
Krt18 |
T |
G |
15: 101,939,888 (GRCm39) |
I362S |
probably damaging |
Het |
Lrrc8d |
G |
A |
5: 105,961,606 (GRCm39) |
R672Q |
probably damaging |
Het |
Ly6f |
G |
A |
15: 75,143,652 (GRCm39) |
V120M |
probably damaging |
Het |
Map3k4 |
A |
G |
17: 12,451,321 (GRCm39) |
V1524A |
possibly damaging |
Het |
Mrgprh |
T |
C |
17: 13,095,889 (GRCm39) |
V43A |
probably benign |
Het |
Mx2 |
A |
T |
16: 97,348,633 (GRCm39) |
M269L |
probably damaging |
Het |
Myrfl |
C |
T |
10: 116,634,535 (GRCm39) |
V620I |
probably benign |
Het |
Nlrp9b |
G |
A |
7: 19,783,381 (GRCm39) |
C908Y |
probably damaging |
Het |
Nyap2 |
T |
A |
1: 81,064,991 (GRCm39) |
M1K |
probably null |
Het |
Olfml3 |
A |
T |
3: 103,644,515 (GRCm39) |
H51Q |
probably benign |
Het |
Or11h6 |
C |
T |
14: 50,880,710 (GRCm39) |
T324I |
possibly damaging |
Het |
Pcdhb1 |
G |
A |
18: 37,399,704 (GRCm39) |
V552I |
probably benign |
Het |
Pm20d1 |
T |
A |
1: 131,734,647 (GRCm39) |
I353N |
possibly damaging |
Het |
Sbk2 |
A |
G |
7: 4,965,966 (GRCm39) |
F73L |
possibly damaging |
Het |
Scn10a |
A |
C |
9: 119,490,298 (GRCm39) |
L548R |
possibly damaging |
Het |
Slc45a2 |
C |
T |
15: 11,027,871 (GRCm39) |
T480I |
probably damaging |
Het |
Slmap |
T |
C |
14: 26,204,117 (GRCm39) |
Y68C |
probably damaging |
Het |
Syde2 |
T |
C |
3: 145,707,093 (GRCm39) |
V611A |
probably benign |
Het |
Sympk |
A |
G |
7: 18,769,814 (GRCm39) |
M164V |
probably benign |
Het |
Syt17 |
T |
C |
7: 118,041,626 (GRCm39) |
S43G |
probably benign |
Het |
Ubr1 |
T |
C |
2: 120,723,651 (GRCm39) |
T1303A |
possibly damaging |
Het |
Vmn2r100 |
A |
G |
17: 19,746,257 (GRCm39) |
Y535C |
possibly 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 |
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 |
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 |
|
Predicted Primers |
PCR Primer
(F):5'- AACTGACCAGGAGCTCTCTC -3'
(R):5'- TCCAGAAGTCTGACTCAGCC -3'
Sequencing Primer
(F):5'- AGCTCTCTCAGGTATGGCCAATG -3'
(R):5'- CAGAAGTCTGACTCAGCCAGAGC -3'
|
Posted On |
2016-07-22 |