Incidental Mutation 'R6628:Kdm5d'
| ID |
524949 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm5d
|
| Ensembl Gene |
ENSMUSG00000056673 |
| Gene Name |
lysine demethylase 5D |
| Synonyms |
Smcy, HY, Jarid1d |
| MMRRC Submission |
044750-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.071)
|
| Stock # |
R6628 (G1)
|
| Quality Score |
221.999 |
|
Status
|
Not validated
|
| Chromosome |
Y |
| Chromosomal Location |
897566-943813 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 900525 bp (GRCm39)
|
| Zygosity |
Homozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 190
(Y190C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000139636
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000055032]
[ENSMUST00000186696]
[ENSMUST00000186726]
[ENSMUST00000189069]
|
| AlphaFold |
Q62240 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000055032
AA Change: Y190C
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: Y190C
| 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 |
noncoding transcript
Transcript: ENSMUST00000185542
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000186696
AA Change: Y190C
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: Y190C
| 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 damaging
Transcript: ENSMUST00000186726
AA Change: Y190C
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000140462
Gene: ENSMUSG00000056673
AA Change: Y190C
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000188910
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000189069
AA Change: Y190C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000139636
Gene: ENSMUSG00000056673
AA Change: Y190C
| 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 |
|
Blast:ARID
|
175 |
298 |
1e-46 |
BLAST |
|
PHD
|
325 |
371 |
8.56e-13 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000189626
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.7%
- 20x: 92.9%
|
| Validation Efficiency |
|
| 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: 28 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts1 |
A |
C |
16: 85,592,713 (GRCm39) |
M565R |
probably benign |
Het |
| Cd4 |
A |
G |
6: 124,856,431 (GRCm39) |
L20P |
unknown |
Het |
| Chrm2 |
G |
T |
6: 36,500,292 (GRCm39) |
V50F |
probably damaging |
Het |
| Clasp2 |
A |
G |
9: 113,725,788 (GRCm39) |
T828A |
probably damaging |
Het |
| Clec4a4 |
A |
G |
6: 122,989,763 (GRCm39) |
K135E |
probably benign |
Het |
| Clmn |
T |
C |
12: 104,740,045 (GRCm39) |
R961G |
probably damaging |
Het |
| Cyp2s1 |
T |
C |
7: 25,514,466 (GRCm39) |
K64E |
probably benign |
Het |
| Dagla |
T |
C |
19: 10,240,591 (GRCm39) |
D213G |
probably damaging |
Het |
| Dsp |
A |
T |
13: 38,351,598 (GRCm39) |
E139V |
possibly damaging |
Het |
| Fam168b |
C |
A |
1: 34,875,822 (GRCm39) |
G21V |
probably damaging |
Het |
| Gtf3c1 |
A |
T |
7: 125,267,246 (GRCm39) |
D928E |
probably benign |
Het |
| Gulo |
T |
C |
14: 66,241,619 (GRCm39) |
K80E |
probably benign |
Het |
| H2-T9 |
T |
C |
17: 36,439,946 (GRCm39) |
S63G |
possibly damaging |
Het |
| Kif27 |
A |
T |
13: 58,502,611 (GRCm39) |
H22Q |
probably damaging |
Het |
| Kmt2c |
T |
C |
5: 25,503,926 (GRCm39) |
D383G |
probably benign |
Het |
| Lmtk2 |
A |
G |
5: 144,111,503 (GRCm39) |
E741G |
probably benign |
Het |
| Mphosph9 |
G |
T |
5: 124,436,825 (GRCm39) |
N506K |
probably damaging |
Het |
| Myo16 |
T |
C |
8: 10,620,638 (GRCm39) |
S1674P |
probably damaging |
Het |
| Or5h26 |
T |
C |
16: 58,988,344 (GRCm39) |
H54R |
probably benign |
Het |
| Or8j3c |
T |
G |
2: 86,253,361 (GRCm39) |
N220H |
probably benign |
Het |
| Pdcd10 |
A |
G |
3: 75,428,378 (GRCm39) |
V82A |
probably damaging |
Het |
| Ptpn11 |
G |
T |
5: 121,272,892 (GRCm39) |
|
probably null |
Het |
| Pxdn |
T |
C |
12: 30,049,917 (GRCm39) |
L475P |
probably damaging |
Het |
| Senp6 |
A |
G |
9: 80,040,236 (GRCm39) |
D781G |
probably damaging |
Het |
| Tbc1d5 |
T |
C |
17: 51,043,236 (GRCm39) |
T751A |
probably benign |
Het |
| Tbx18 |
A |
T |
9: 87,597,588 (GRCm39) |
Y315* |
probably null |
Het |
| Wrap53 |
T |
C |
11: 69,452,970 (GRCm39) |
K446E |
probably benign |
Het |
| Wwp1 |
T |
C |
4: 19,661,963 (GRCm39) |
|
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 |
|
|
R6745:Kdm5d
|
UTSW |
Y |
927,112 (GRCm39) |
missense |
probably benign |
0.28 |
|
R6867:Kdm5d
|
UTSW |
Y |
927,425 (GRCm39) |
missense |
probably benign |
|
|
R6963:Kdm5d
|
UTSW |
Y |
937,975 (GRCm39) |
missense |
probably benign |
0.01 |
|
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'- TGGTCAGTAAACTTTAGTGAGTTCC -3'
(R):5'- TAACACTGGCAGCTTATTAGAAGG -3'
Sequencing Primer
(F):5'- AGAAGTGCAATTACATCAGGTTG -3'
(R):5'- TCCTCGTCTACTGTAGCA -3'
|
| Posted On |
2018-06-22 |
Incidental Mutation