Incidental Mutation 'R6963:Kdm5d'
ID |
543347 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm5d
|
Ensembl Gene |
ENSMUSG00000056673 |
Gene Name |
lysine demethylase 5D |
Synonyms |
Smcy, HY, Jarid1d |
MMRRC Submission |
045073-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.071)
|
Stock # |
R6963 (G1)
|
Quality Score |
221.999 |
Status
|
Validated
|
Chromosome |
Y |
Chromosomal Location |
897566-943813 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to A
at 937975 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamine to Lysine
at position 925
(Q925K)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000061095
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000055032]
[ENSMUST00000186696]
[ENSMUST00000186726]
|
AlphaFold |
Q62240 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000055032
AA Change: Q925K
PolyPhen 2
Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
|
SMART Domains |
Protein: ENSMUSP00000061095 Gene: ENSMUSG00000056673 AA Change: Q925K
Domain | Start | End | E-Value | Type |
JmjN
|
13 |
54 |
3.45e-23 |
SMART |
ARID
|
76 |
165 |
4.84e-36 |
SMART |
BRIGHT
|
80 |
170 |
4.48e-38 |
SMART |
PHD
|
325 |
371 |
8.56e-13 |
SMART |
JmjC
|
467 |
633 |
2.52e-63 |
SMART |
Pfam:zf-C5HC2
|
706 |
758 |
5.2e-18 |
PFAM |
Pfam:PLU-1
|
771 |
1096 |
1.4e-89 |
PFAM |
low complexity region
|
1147 |
1156 |
N/A |
INTRINSIC |
low complexity region
|
1164 |
1181 |
N/A |
INTRINSIC |
PHD
|
1182 |
1243 |
2.54e-6 |
SMART |
coiled coil region
|
1290 |
1318 |
N/A |
INTRINSIC |
low complexity region
|
1340 |
1351 |
N/A |
INTRINSIC |
low complexity region
|
1395 |
1406 |
N/A |
INTRINSIC |
low complexity region
|
1453 |
1459 |
N/A |
INTRINSIC |
low complexity region
|
1525 |
1541 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000186696
|
SMART Domains |
Protein: ENSMUSP00000140663 Gene: ENSMUSG00000056673
Domain | Start | End | E-Value | Type |
JmjN
|
13 |
54 |
3.45e-23 |
SMART |
ARID
|
76 |
165 |
4.84e-36 |
SMART |
BRIGHT
|
80 |
170 |
4.48e-38 |
SMART |
PHD
|
325 |
371 |
8.56e-13 |
SMART |
JmjC
|
467 |
633 |
2.52e-63 |
SMART |
low complexity region
|
675 |
689 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000186726
|
SMART Domains |
Protein: ENSMUSP00000140462 Gene: ENSMUSG00000056673
Domain | Start | End | E-Value | Type |
JmjN
|
13 |
54 |
1.4e-25 |
SMART |
ARID
|
76 |
165 |
3.8e-40 |
SMART |
BRIGHT
|
80 |
170 |
2.3e-40 |
SMART |
Blast:ARID
|
175 |
260 |
1e-41 |
BLAST |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.5%
|
Validation Efficiency |
100% (41/41) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 41 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Aasdh |
G |
A |
5: 77,044,303 (GRCm39) |
H196Y |
probably damaging |
Het |
Abi3 |
G |
A |
11: 95,723,567 (GRCm39) |
|
probably benign |
Het |
Adgrb2 |
CG |
C |
4: 129,908,155 (GRCm39) |
|
probably null |
Het |
Asgr1 |
T |
C |
11: 69,946,794 (GRCm39) |
|
probably null |
Het |
Atp2c2 |
C |
T |
8: 120,457,006 (GRCm39) |
R203* |
probably null |
Het |
Brms1 |
T |
A |
19: 5,096,681 (GRCm39) |
I121N |
probably damaging |
Het |
Ccdc149 |
G |
A |
5: 52,596,439 (GRCm39) |
R58W |
probably damaging |
Het |
D630003M21Rik |
T |
C |
2: 158,042,228 (GRCm39) |
E906G |
probably benign |
Het |
Enpp5 |
G |
A |
17: 44,396,155 (GRCm39) |
G356S |
probably damaging |
Het |
Fry |
A |
G |
5: 150,381,309 (GRCm39) |
T444A |
probably benign |
Het |
Ggn |
A |
G |
7: 28,871,007 (GRCm39) |
E142G |
probably damaging |
Het |
Gm5150 |
A |
G |
3: 16,060,555 (GRCm39) |
|
probably benign |
Het |
Gm57858 |
A |
G |
3: 36,104,811 (GRCm39) |
Y17H |
probably benign |
Het |
Gp2 |
A |
G |
7: 119,052,120 (GRCm39) |
V198A |
probably benign |
Het |
Gstm3 |
A |
G |
3: 107,874,940 (GRCm39) |
V104A |
probably benign |
Het |
Idua |
A |
G |
5: 108,827,641 (GRCm39) |
K152E |
possibly damaging |
Het |
Igsf21 |
A |
G |
4: 139,755,041 (GRCm39) |
S443P |
probably benign |
Het |
Ly6k |
G |
C |
15: 74,670,431 (GRCm39) |
P37R |
probably damaging |
Het |
Mcm9 |
A |
G |
10: 53,424,713 (GRCm39) |
S626P |
probably damaging |
Het |
Mcoln2 |
A |
G |
3: 145,877,790 (GRCm39) |
K137R |
probably damaging |
Het |
Mctp2 |
T |
C |
7: 71,877,804 (GRCm39) |
N298S |
probably damaging |
Het |
Myo10 |
T |
C |
15: 25,734,149 (GRCm39) |
I379T |
probably benign |
Het |
Myo15b |
G |
T |
11: 115,781,540 (GRCm39) |
|
probably null |
Het |
Nrg1 |
A |
G |
8: 32,407,690 (GRCm39) |
F181S |
probably benign |
Het |
Or5b24 |
C |
T |
19: 12,913,002 (GRCm39) |
A300V |
probably damaging |
Het |
Pals2 |
T |
C |
6: 50,140,635 (GRCm39) |
|
probably null |
Het |
Pde9a |
G |
T |
17: 31,662,861 (GRCm39) |
V97L |
probably benign |
Het |
Rfc5 |
T |
A |
5: 117,525,931 (GRCm39) |
|
probably null |
Het |
Rnf145 |
T |
C |
11: 44,455,104 (GRCm39) |
S662P |
probably benign |
Het |
Rsf1 |
G |
A |
7: 97,229,117 (GRCm39) |
|
probably benign |
Het |
Scfd2 |
A |
G |
5: 74,642,870 (GRCm39) |
V359A |
probably damaging |
Het |
Skp2 |
T |
C |
15: 9,139,515 (GRCm39) |
|
probably null |
Het |
St3gal1 |
A |
G |
15: 66,983,195 (GRCm39) |
V187A |
possibly damaging |
Het |
Tekt2 |
T |
C |
4: 126,218,110 (GRCm39) |
E134G |
probably damaging |
Het |
Ttll4 |
T |
A |
1: 74,720,975 (GRCm39) |
I547K |
probably damaging |
Het |
Vmn1r4 |
T |
C |
6: 56,933,769 (GRCm39) |
I91T |
probably damaging |
Het |
Vmn2r93 |
T |
C |
17: 18,536,849 (GRCm39) |
S511P |
probably damaging |
Het |
Vps50 |
T |
C |
6: 3,592,577 (GRCm39) |
|
probably null |
Het |
Zeb2 |
T |
G |
2: 44,878,811 (GRCm39) |
E1141A |
probably damaging |
Het |
Zfp1002 |
A |
G |
2: 150,097,265 (GRCm39) |
C55R |
probably damaging |
Het |
Zfp326 |
T |
A |
5: 106,059,359 (GRCm39) |
Y373* |
probably null |
Het |
|
Other mutations in Kdm5d |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
R0013:Kdm5d
|
UTSW |
Y |
941,715 (GRCm39) |
missense |
probably benign |
0.37 |
R0013:Kdm5d
|
UTSW |
Y |
941,715 (GRCm39) |
missense |
probably benign |
0.37 |
R0426:Kdm5d
|
UTSW |
Y |
942,437 (GRCm39) |
splice site |
probably benign |
|
R0486:Kdm5d
|
UTSW |
Y |
927,107 (GRCm39) |
missense |
probably damaging |
1.00 |
R0620:Kdm5d
|
UTSW |
Y |
927,330 (GRCm39) |
missense |
probably damaging |
0.98 |
R0781:Kdm5d
|
UTSW |
Y |
910,539 (GRCm39) |
missense |
probably damaging |
1.00 |
R1015:Kdm5d
|
UTSW |
Y |
941,687 (GRCm39) |
missense |
possibly damaging |
0.95 |
R1110:Kdm5d
|
UTSW |
Y |
910,539 (GRCm39) |
missense |
probably damaging |
1.00 |
R1163:Kdm5d
|
UTSW |
Y |
898,029 (GRCm39) |
missense |
probably benign |
0.18 |
R1203:Kdm5d
|
UTSW |
Y |
941,011 (GRCm39) |
missense |
probably damaging |
1.00 |
R1238:Kdm5d
|
UTSW |
Y |
941,282 (GRCm39) |
missense |
probably damaging |
1.00 |
R1723:Kdm5d
|
UTSW |
Y |
927,753 (GRCm39) |
missense |
probably damaging |
1.00 |
R1842:Kdm5d
|
UTSW |
Y |
927,798 (GRCm39) |
missense |
probably damaging |
1.00 |
R1885:Kdm5d
|
UTSW |
Y |
940,781 (GRCm39) |
splice site |
probably null |
|
R2131:Kdm5d
|
UTSW |
Y |
941,483 (GRCm39) |
missense |
probably benign |
0.02 |
R2571:Kdm5d
|
UTSW |
Y |
940,932 (GRCm39) |
missense |
probably benign |
0.11 |
R2931:Kdm5d
|
UTSW |
Y |
942,992 (GRCm39) |
missense |
probably benign |
0.18 |
R3123:Kdm5d
|
UTSW |
Y |
900,558 (GRCm39) |
missense |
possibly damaging |
0.63 |
R3919:Kdm5d
|
UTSW |
Y |
939,914 (GRCm39) |
missense |
probably damaging |
1.00 |
R4018:Kdm5d
|
UTSW |
Y |
910,441 (GRCm39) |
splice site |
probably benign |
|
R4031:Kdm5d
|
UTSW |
Y |
916,910 (GRCm39) |
missense |
probably damaging |
1.00 |
R4403:Kdm5d
|
UTSW |
Y |
899,830 (GRCm39) |
missense |
probably damaging |
1.00 |
R4571:Kdm5d
|
UTSW |
Y |
927,110 (GRCm39) |
missense |
probably damaging |
1.00 |
R4583:Kdm5d
|
UTSW |
Y |
914,134 (GRCm39) |
missense |
probably damaging |
1.00 |
R4962:Kdm5d
|
UTSW |
Y |
940,624 (GRCm39) |
missense |
probably damaging |
1.00 |
R5105:Kdm5d
|
UTSW |
Y |
941,752 (GRCm39) |
missense |
probably benign |
0.00 |
R5249:Kdm5d
|
UTSW |
Y |
916,692 (GRCm39) |
missense |
probably damaging |
1.00 |
R5367:Kdm5d
|
UTSW |
Y |
941,645 (GRCm39) |
missense |
probably benign |
0.05 |
R5373:Kdm5d
|
UTSW |
Y |
927,995 (GRCm39) |
missense |
probably benign |
0.09 |
R5374:Kdm5d
|
UTSW |
Y |
927,995 (GRCm39) |
missense |
probably benign |
0.09 |
R5876:Kdm5d
|
UTSW |
Y |
900,525 (GRCm39) |
missense |
probably damaging |
1.00 |
R5909:Kdm5d
|
UTSW |
Y |
941,306 (GRCm39) |
missense |
probably benign |
0.01 |
R6014:Kdm5d
|
UTSW |
Y |
921,528 (GRCm39) |
missense |
probably benign |
0.45 |
R6109:Kdm5d
|
UTSW |
Y |
921,501 (GRCm39) |
missense |
probably damaging |
1.00 |
R6251:Kdm5d
|
UTSW |
Y |
921,693 (GRCm39) |
missense |
probably damaging |
1.00 |
R6349:Kdm5d
|
UTSW |
Y |
916,847 (GRCm39) |
missense |
probably damaging |
0.99 |
R6450:Kdm5d
|
UTSW |
Y |
927,056 (GRCm39) |
missense |
probably damaging |
1.00 |
R6595:Kdm5d
|
UTSW |
Y |
939,829 (GRCm39) |
missense |
probably benign |
|
R6628:Kdm5d
|
UTSW |
Y |
900,525 (GRCm39) |
missense |
probably damaging |
1.00 |
R6745:Kdm5d
|
UTSW |
Y |
927,112 (GRCm39) |
missense |
probably benign |
0.28 |
R6867:Kdm5d
|
UTSW |
Y |
927,425 (GRCm39) |
missense |
probably benign |
|
R7163:Kdm5d
|
UTSW |
Y |
899,940 (GRCm39) |
missense |
probably damaging |
1.00 |
R7374:Kdm5d
|
UTSW |
Y |
941,491 (GRCm39) |
missense |
probably benign |
0.41 |
R7483:Kdm5d
|
UTSW |
Y |
914,044 (GRCm39) |
missense |
possibly damaging |
0.50 |
R7501:Kdm5d
|
UTSW |
Y |
941,488 (GRCm39) |
missense |
probably damaging |
1.00 |
R7815:Kdm5d
|
UTSW |
Y |
940,702 (GRCm39) |
missense |
probably damaging |
1.00 |
R7835:Kdm5d
|
UTSW |
Y |
900,558 (GRCm39) |
missense |
possibly damaging |
0.63 |
R8057:Kdm5d
|
UTSW |
Y |
927,355 (GRCm39) |
missense |
possibly damaging |
0.48 |
R8080:Kdm5d
|
UTSW |
Y |
910,742 (GRCm39) |
missense |
probably benign |
0.01 |
R8130:Kdm5d
|
UTSW |
Y |
940,658 (GRCm39) |
missense |
possibly damaging |
0.75 |
R8213:Kdm5d
|
UTSW |
Y |
941,515 (GRCm39) |
missense |
probably damaging |
1.00 |
R8261:Kdm5d
|
UTSW |
Y |
936,929 (GRCm39) |
missense |
probably damaging |
0.99 |
R8344:Kdm5d
|
UTSW |
Y |
942,477 (GRCm39) |
missense |
probably benign |
0.05 |
R8348:Kdm5d
|
UTSW |
Y |
914,056 (GRCm39) |
missense |
probably benign |
0.00 |
R8445:Kdm5d
|
UTSW |
Y |
916,874 (GRCm39) |
missense |
probably damaging |
1.00 |
R8448:Kdm5d
|
UTSW |
Y |
914,056 (GRCm39) |
missense |
probably benign |
0.00 |
R8754:Kdm5d
|
UTSW |
Y |
941,594 (GRCm39) |
missense |
probably damaging |
1.00 |
R9203:Kdm5d
|
UTSW |
Y |
940,981 (GRCm39) |
missense |
probably damaging |
0.99 |
R9259:Kdm5d
|
UTSW |
Y |
942,640 (GRCm39) |
missense |
possibly damaging |
0.84 |
R9541:Kdm5d
|
UTSW |
Y |
910,801 (GRCm39) |
missense |
probably damaging |
1.00 |
R9668:Kdm5d
|
UTSW |
Y |
943,075 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
Predicted Primers |
PCR Primer
(F):5'- TTTGCAGGATGTTCTTCAACAG -3'
(R):5'- TGAAGCAGACTCAATAAAGGCC -3'
Sequencing Primer
(F):5'- CAGGATGTTCTTCAACAGGTGGAATC -3'
(R):5'- AGCAAAAATGGGCCTTTTCCTC -3'
|
Posted On |
2018-11-28 |