Incidental Mutation 'R1238:Kdm5d'
| ID |
152519 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm5d
|
| Ensembl Gene |
ENSMUSG00000056673 |
| Gene Name |
lysine demethylase 5D |
| Synonyms |
Smcy, HY, Jarid1d |
| MMRRC Submission |
039305-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.071)
|
| Stock # |
R1238 (G1)
|
| Quality Score |
222 |
|
Status
|
Validated
|
| Chromosome |
Y |
| Chromosomal Location |
897566-943813 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 941282 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Histidine
at position 1161
(R1161H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000061095
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000055032]
[ENSMUST00000186696]
[ENSMUST00000186726]
|
| AlphaFold |
Q62240 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000055032
AA Change: R1161H
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: R1161H
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000187296
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000189955
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.2%
- 20x: 92.2%
|
| Validation Efficiency |
97% (35/36) |
| 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: 35 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc4 |
G |
A |
14: 118,835,051 (GRCm39) |
|
probably benign |
Het |
| BC051665 |
T |
A |
13: 60,932,451 (GRCm39) |
N78I |
probably damaging |
Het |
| Cacna1c |
C |
T |
6: 118,589,586 (GRCm39) |
R1446H |
probably damaging |
Het |
| Cep290 |
A |
C |
10: 100,353,725 (GRCm39) |
Q819H |
probably damaging |
Het |
| Cep70 |
T |
C |
9: 99,136,318 (GRCm39) |
I7T |
probably benign |
Het |
| Chd1l |
C |
T |
3: 97,490,047 (GRCm39) |
E503K |
probably benign |
Het |
| Cit |
T |
A |
5: 115,989,280 (GRCm39) |
F56I |
probably benign |
Het |
| Colec10 |
T |
C |
15: 54,325,835 (GRCm39) |
F222L |
possibly damaging |
Het |
| Crocc |
G |
A |
4: 140,762,675 (GRCm39) |
A769V |
probably benign |
Het |
| Ctcf |
T |
C |
8: 106,397,909 (GRCm39) |
|
probably benign |
Het |
| Ect2l |
T |
C |
10: 18,018,852 (GRCm39) |
R607G |
possibly damaging |
Het |
| Efcab6 |
T |
G |
15: 83,817,338 (GRCm39) |
E745A |
probably benign |
Het |
| Eif1ad |
T |
G |
19: 5,420,111 (GRCm39) |
*171G |
probably null |
Het |
| Gvin-ps6 |
A |
G |
7: 106,022,264 (GRCm39) |
V246A |
probably damaging |
Het |
| H2-D1 |
A |
G |
17: 35,482,908 (GRCm39) |
D146G |
probably damaging |
Het |
| Iqub |
C |
T |
6: 24,505,884 (GRCm39) |
R8H |
probably benign |
Het |
| Itih4 |
A |
T |
14: 30,609,906 (GRCm39) |
I79F |
probably damaging |
Het |
| Map4 |
T |
C |
9: 109,897,648 (GRCm39) |
S675P |
probably benign |
Het |
| Mfsd4b3-ps |
A |
T |
10: 39,823,222 (GRCm39) |
V346E |
probably damaging |
Het |
| Or1j21 |
A |
T |
2: 36,683,601 (GRCm39) |
M118L |
probably damaging |
Het |
| Or2ad1 |
C |
T |
13: 21,326,337 (GRCm39) |
V297I |
probably benign |
Het |
| Or7d11 |
T |
A |
9: 19,966,757 (GRCm39) |
M1L |
probably benign |
Het |
| P2rx1 |
A |
C |
11: 72,903,784 (GRCm39) |
K282T |
probably damaging |
Het |
| Parp14 |
G |
A |
16: 35,677,130 (GRCm39) |
A946V |
probably benign |
Het |
| Pdia3 |
G |
A |
2: 121,262,858 (GRCm39) |
G275S |
probably damaging |
Het |
| Ptprj |
A |
T |
2: 90,274,758 (GRCm39) |
|
probably null |
Het |
| Pwp1 |
A |
G |
10: 85,721,726 (GRCm39) |
I411V |
probably benign |
Het |
| Rnaset2b |
T |
C |
17: 7,256,169 (GRCm39) |
S12P |
probably damaging |
Het |
| Rrs1 |
C |
A |
1: 9,616,026 (GRCm39) |
|
probably null |
Het |
| Ryr2 |
T |
C |
13: 11,774,589 (GRCm39) |
E1189G |
probably damaging |
Het |
| Slc25a21 |
T |
A |
12: 56,785,272 (GRCm39) |
I202F |
probably benign |
Het |
| Tcfl5 |
A |
G |
2: 180,264,440 (GRCm39) |
V472A |
probably benign |
Het |
| Ttc12 |
A |
T |
9: 49,369,487 (GRCm39) |
|
probably benign |
Het |
| Ugt2b1 |
T |
G |
5: 87,073,988 (GRCm39) |
I124L |
probably benign |
Het |
| Usp14 |
A |
T |
18: 9,997,763 (GRCm39) |
N357K |
probably benign |
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 |
|
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 |
|
|
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'- TGTGGTAAGCAGCTTGACACAGAG -3'
(R):5'- CCAGCAATGACAAGATGGTCTCCAG -3'
Sequencing Primer
(F):5'- CTTATGGGTATCTCACTGAGAAGAAG -3'
(R):5'- ACAGGAACTTGGTGTCCCATTC -3'
|
| Posted On |
2014-01-29 |
Incidental Mutation