Incidental Mutation 'R7835:Kdm5d'
| ID |
605945 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm5d
|
| Ensembl Gene |
ENSMUSG00000056673 |
| Gene Name |
lysine demethylase 5D |
| Synonyms |
Smcy, HY, Jarid1d |
| MMRRC Submission |
045889-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.071)
|
| Stock # |
R7835 (G1)
|
| Quality Score |
221.999 |
|
Status
|
Validated
|
| Chromosome |
Y |
| Chromosomal Location |
897566-943813 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 900558 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 201
(V201A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000139636
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000055032]
[ENSMUST00000186696]
[ENSMUST00000186726]
[ENSMUST00000189069]
|
| AlphaFold |
Q62240 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000055032
AA Change: V201A
PolyPhen 2
Score 0.387 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: V201A
| 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 benign
Transcript: ENSMUST00000186696
AA Change: V201A
PolyPhen 2
Score 0.116 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: V201A
| 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
AA Change: V201A
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000140462
Gene: ENSMUSG00000056673
AA Change: V201A
| 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 |
possibly damaging
Transcript: ENSMUST00000189069
AA Change: V201A
PolyPhen 2
Score 0.635 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000139636
Gene: ENSMUSG00000056673
AA Change: V201A
| 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
|
| Meta Mutation Damage Score |
0.1795 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 98.9%
|
| Validation Efficiency |
98% (48/49) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acan |
T |
A |
7: 78,749,623 (GRCm39) |
S1465T |
probably benign |
Het |
| Accsl |
T |
A |
2: 93,696,329 (GRCm39) |
K90* |
probably null |
Het |
| Adamts3 |
A |
T |
5: 89,848,299 (GRCm39) |
D674E |
possibly damaging |
Het |
| Adap2 |
T |
A |
11: 80,051,057 (GRCm39) |
V129D |
probably benign |
Het |
| Ank3 |
A |
G |
10: 69,823,557 (GRCm39) |
D742G |
|
Het |
| C1ra |
G |
A |
6: 124,494,684 (GRCm39) |
E316K |
probably benign |
Het |
| Cachd1 |
G |
T |
4: 100,831,350 (GRCm39) |
|
probably null |
Het |
| Ccne1 |
G |
T |
7: 37,802,270 (GRCm39) |
Q133K |
probably benign |
Het |
| Cers3 |
C |
T |
7: 66,423,387 (GRCm39) |
H111Y |
possibly damaging |
Het |
| Chst5 |
A |
T |
8: 112,617,234 (GRCm39) |
L129M |
probably damaging |
Het |
| Depdc7 |
A |
G |
2: 104,558,530 (GRCm39) |
S164P |
probably benign |
Het |
| Dnah10 |
G |
A |
5: 124,854,298 (GRCm39) |
A1966T |
probably damaging |
Het |
| Fcgbp |
T |
G |
7: 27,816,632 (GRCm39) |
S2365A |
possibly damaging |
Het |
| Ihh |
A |
G |
1: 74,985,525 (GRCm39) |
V320A |
probably damaging |
Het |
| Kif13b |
T |
A |
14: 65,004,901 (GRCm39) |
H1117Q |
probably benign |
Het |
| Lcn8 |
C |
A |
2: 25,545,308 (GRCm39) |
|
probably null |
Het |
| Lrp4 |
T |
C |
2: 91,325,387 (GRCm39) |
V1404A |
possibly damaging |
Het |
| Lrrc61 |
A |
T |
6: 48,545,506 (GRCm39) |
T110S |
probably benign |
Het |
| Mrpl19 |
G |
A |
6: 81,939,107 (GRCm39) |
R232C |
probably damaging |
Het |
| Muc5ac |
G |
C |
7: 141,363,040 (GRCm39) |
G2117A |
unknown |
Het |
| Mzt1 |
T |
C |
14: 99,283,439 (GRCm39) |
T21A |
probably benign |
Het |
| Naip6 |
G |
T |
13: 100,452,512 (GRCm39) |
A183E |
probably benign |
Het |
| Neb |
T |
C |
2: 52,040,589 (GRCm39) |
D6624G |
probably benign |
Het |
| Nup85 |
A |
G |
11: 115,460,897 (GRCm39) |
D183G |
probably benign |
Het |
| Olfm5 |
A |
T |
7: 103,803,652 (GRCm39) |
Y195* |
probably null |
Het |
| Or7g16 |
T |
A |
9: 18,727,105 (GRCm39) |
M162L |
probably benign |
Het |
| Piezo2 |
A |
T |
18: 63,216,016 (GRCm39) |
F1216I |
probably benign |
Het |
| Pkd1l3 |
GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA |
GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA |
8: 110,350,827 (GRCm39) |
|
probably benign |
Het |
| Polr1a |
T |
C |
6: 71,892,126 (GRCm39) |
V135A |
probably benign |
Het |
| Ppcdc |
A |
G |
9: 57,327,559 (GRCm39) |
S83P |
probably benign |
Het |
| Prss21 |
A |
T |
17: 24,088,425 (GRCm39) |
Q130L |
possibly damaging |
Het |
| Rdx |
T |
A |
9: 51,977,088 (GRCm39) |
N112K |
probably damaging |
Het |
| Rgs22 |
A |
G |
15: 36,082,057 (GRCm39) |
|
probably null |
Het |
| Rps23rg1 |
A |
G |
8: 3,630,452 (GRCm39) |
|
probably benign |
Het |
| Rps26 |
C |
T |
10: 128,461,995 (GRCm39) |
V40I |
probably benign |
Het |
| Runx2 |
A |
T |
17: 44,919,123 (GRCm39) |
M405K |
probably damaging |
Het |
| Serinc2 |
A |
C |
4: 130,169,280 (GRCm39) |
C4G |
unknown |
Het |
| Sh3rf2 |
C |
A |
18: 42,244,235 (GRCm39) |
R266S |
probably benign |
Het |
| Slc38a10 |
A |
G |
11: 120,007,822 (GRCm39) |
I386T |
possibly damaging |
Het |
| Stab2 |
G |
A |
10: 86,708,483 (GRCm39) |
P1694L |
probably benign |
Het |
| Taf4 |
G |
A |
2: 179,573,822 (GRCm39) |
T682M |
probably damaging |
Het |
| Tasor |
G |
T |
14: 27,198,600 (GRCm39) |
G1311C |
probably damaging |
Het |
| Tmem102 |
A |
G |
11: 69,695,171 (GRCm39) |
V267A |
probably damaging |
Het |
| Trim65 |
A |
G |
11: 116,021,755 (GRCm39) |
L26P |
probably damaging |
Het |
| Vmn1r160 |
T |
A |
7: 22,571,379 (GRCm39) |
M244K |
possibly damaging |
Het |
| Vmn1r57 |
A |
T |
7: 5,224,138 (GRCm39) |
H221L |
probably benign |
Het |
| Wdr89 |
C |
A |
12: 75,679,673 (GRCm39) |
V194F |
probably damaging |
Het |
| Wee1 |
C |
A |
7: 109,730,085 (GRCm39) |
Y396* |
probably null |
Het |
| Zfp451 |
A |
T |
1: 33,812,060 (GRCm39) |
V885D |
probably damaging |
Het |
| Zfp981 |
A |
T |
4: 146,622,333 (GRCm39) |
Q419H |
probably benign |
Het |
| Znfx1 |
A |
G |
2: 166,881,747 (GRCm39) |
Y1081H |
probably damaging |
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 |
|
|
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 |
|
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'- GTGTTCAAAATGAGTAAGCTGGT -3'
(R):5'- CATTTCCCATTGGTTTCAACTTAGA -3'
Sequencing Primer
(F):5'- AAGCTGGTATTACTTTTGTTTAGCTG -3'
(R):5'- TCCCATTGGTTTCAACTTAGATATTC -3'
|
| Posted On |
2019-12-20 |
Incidental Mutation