Incidental Mutation 'R5105:Kdm5d'
ID |
402011 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm5d
|
Ensembl Gene |
ENSMUSG00000056673 |
Gene Name |
lysine demethylase 5D |
Synonyms |
Smcy, HY, Jarid1d |
MMRRC Submission |
042693-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.071)
|
Stock # |
R5105 (G1)
|
Quality Score |
222 |
Status
|
Validated
|
Chromosome |
Y |
Chromosomal Location |
897566-943813 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 941752 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Lysine to Glutamic Acid
at position 1318
(K1318E)
|
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: K1318E
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
SMART Domains |
Protein: ENSMUSP00000061095 Gene: ENSMUSG00000056673 AA Change: K1318E
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 |
0.0898 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.8%
|
Validation Efficiency |
96% (52/54) |
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: 47 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Btbd8 |
T |
G |
5: 107,658,337 (GRCm39) |
S1124A |
possibly damaging |
Het |
Camsap1 |
A |
G |
2: 25,830,941 (GRCm39) |
S445P |
probably damaging |
Het |
Ccdc92 |
G |
A |
5: 124,912,858 (GRCm39) |
P224S |
probably damaging |
Het |
Cep135 |
T |
C |
5: 76,741,939 (GRCm39) |
V125A |
probably benign |
Het |
Cep192 |
T |
A |
18: 67,999,612 (GRCm39) |
C2159S |
probably benign |
Het |
Col1a1 |
G |
T |
11: 94,833,211 (GRCm39) |
R404L |
unknown |
Het |
Col6a3 |
A |
T |
1: 90,725,862 (GRCm39) |
M1382K |
possibly damaging |
Het |
Cyp4a12b |
T |
C |
4: 115,290,958 (GRCm39) |
S329P |
probably damaging |
Het |
Dclk1 |
T |
G |
3: 55,163,360 (GRCm39) |
S151A |
probably benign |
Het |
Ddhd1 |
A |
T |
14: 45,894,864 (GRCm39) |
V202E |
probably benign |
Het |
Dlx6 |
AGG |
AG |
6: 6,865,180 (GRCm39) |
|
probably null |
Het |
Dnah10 |
A |
G |
5: 124,888,546 (GRCm39) |
E3050G |
probably benign |
Het |
Dync1h1 |
T |
A |
12: 110,584,366 (GRCm39) |
F590I |
probably damaging |
Het |
Eif4b |
T |
C |
15: 101,992,631 (GRCm39) |
Y63H |
probably benign |
Het |
Fscb |
T |
C |
12: 64,520,110 (GRCm39) |
E452G |
possibly damaging |
Het |
Gpx3 |
A |
T |
11: 54,797,980 (GRCm39) |
T39S |
possibly damaging |
Het |
Grin2b |
T |
A |
6: 135,709,439 (GRCm39) |
Y1369F |
probably benign |
Het |
Kank4 |
A |
T |
4: 98,667,396 (GRCm39) |
N350K |
probably benign |
Het |
Large1 |
A |
T |
8: 73,578,872 (GRCm39) |
Y444* |
probably null |
Het |
Lhx3 |
TCCTACGGGCCGGCCC |
TCC |
2: 26,091,435 (GRCm39) |
|
probably null |
Het |
Lrrc47 |
A |
G |
4: 154,096,673 (GRCm39) |
Q156R |
probably damaging |
Het |
Lrriq4 |
T |
C |
3: 30,704,632 (GRCm39) |
L220P |
probably damaging |
Het |
Matn2 |
A |
G |
15: 34,355,814 (GRCm39) |
D273G |
possibly damaging |
Het |
Myo18b |
T |
A |
5: 112,988,644 (GRCm39) |
I981F |
probably damaging |
Het |
Or1q1 |
G |
A |
2: 36,887,469 (GRCm39) |
|
probably null |
Het |
Or2n1c |
A |
C |
17: 38,519,208 (GRCm39) |
E24A |
possibly damaging |
Het |
Or5aq1 |
A |
G |
2: 86,966,554 (GRCm39) |
I37T |
probably benign |
Het |
Or6b13 |
A |
G |
7: 139,782,462 (GRCm39) |
Y74H |
probably damaging |
Het |
Or8d6 |
T |
C |
9: 39,853,694 (GRCm39) |
V46A |
probably benign |
Het |
Pkdrej |
T |
C |
15: 85,700,585 (GRCm39) |
T1784A |
probably damaging |
Het |
Ppp3cb |
A |
G |
14: 20,559,490 (GRCm39) |
V422A |
possibly damaging |
Het |
Rlf |
G |
A |
4: 121,007,564 (GRCm39) |
T472I |
probably damaging |
Het |
Scaf11 |
T |
C |
15: 96,318,313 (GRCm39) |
E417G |
probably damaging |
Het |
Shisa2 |
A |
T |
14: 59,867,263 (GRCm39) |
T172S |
possibly damaging |
Het |
Siglec1 |
T |
A |
2: 130,922,320 (GRCm39) |
Q585L |
possibly damaging |
Het |
Sorcs1 |
A |
T |
19: 50,213,579 (GRCm39) |
M716K |
possibly damaging |
Het |
Sparcl1 |
C |
T |
5: 104,233,629 (GRCm39) |
M573I |
probably damaging |
Het |
Stxbp5l |
C |
A |
16: 36,962,734 (GRCm39) |
V774F |
probably benign |
Het |
Tcaf3 |
A |
G |
6: 42,568,259 (GRCm39) |
F699S |
probably damaging |
Het |
Tmem87b |
T |
C |
2: 128,673,509 (GRCm39) |
V251A |
probably damaging |
Het |
Trpc6 |
T |
A |
9: 8,649,471 (GRCm39) |
N560K |
probably benign |
Het |
Trpv4 |
T |
A |
5: 114,764,981 (GRCm39) |
I678F |
probably damaging |
Het |
Ttc3 |
A |
T |
16: 94,267,793 (GRCm39) |
H1935L |
possibly damaging |
Het |
Vmn2r59 |
T |
A |
7: 41,696,529 (GRCm39) |
Y71F |
probably benign |
Het |
Wdfy3 |
A |
G |
5: 102,003,415 (GRCm39) |
I2900T |
probably damaging |
Het |
Zfp184 |
A |
G |
13: 22,143,799 (GRCm39) |
T502A |
possibly damaging |
Het |
Zmym6 |
A |
G |
4: 127,017,551 (GRCm39) |
I1019V |
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 |
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 |
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'- GAGACTGTCTGTAAGGCTACC -3'
(R):5'- ACTGAGAACCACTGATACATGAGAG -3'
Sequencing Primer
(F):5'- ACTGTCTGTAAGGCTACCTGAGG -3'
(R):5'- CCACTGATACATGAGAGTGCTATG -3'
|
Posted On |
2016-07-22 |