Incidental Mutation 'R6343:Kdm5a'
| ID |
513999 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm5a
|
| Ensembl Gene |
ENSMUSG00000030180 |
| Gene Name |
lysine demethylase 5A |
| Synonyms |
Rbbp2, Jarid1a, RBP2 |
| MMRRC Submission |
044497-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6343 (G1)
|
| Quality Score |
165.009 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
120341085-120421535 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 120359894 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 230
(V230A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000005108
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000005108]
[ENSMUST00000132009]
[ENSMUST00000135802]
[ENSMUST00000203373]
|
| AlphaFold |
Q3UXZ9 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000005108
AA Change: V230A
PolyPhen 2
Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: V230A
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
18 |
59 |
4.06e-20 |
SMART |
|
ARID
|
81 |
170 |
4.76e-35 |
SMART |
|
BRIGHT
|
85 |
175 |
2.48e-31 |
SMART |
|
PHD
|
295 |
341 |
1.16e-14 |
SMART |
|
Blast:JmjC
|
384 |
436 |
2e-22 |
BLAST |
|
JmjC
|
437 |
603 |
5.88e-73 |
SMART |
|
low complexity region
|
638 |
651 |
N/A |
INTRINSIC |
|
Pfam:zf-C5HC2
|
676 |
729 |
1.3e-21 |
PFAM |
|
Pfam:PLU-1
|
740 |
1072 |
1.2e-104 |
PFAM |
|
low complexity region
|
1091 |
1119 |
N/A |
INTRINSIC |
|
PHD
|
1163 |
1216 |
1.37e-11 |
SMART |
|
low complexity region
|
1269 |
1280 |
N/A |
INTRINSIC |
|
low complexity region
|
1337 |
1351 |
N/A |
INTRINSIC |
|
low complexity region
|
1403 |
1414 |
N/A |
INTRINSIC |
|
low complexity region
|
1494 |
1512 |
N/A |
INTRINSIC |
|
coiled coil region
|
1534 |
1579 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000122505
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000132009
AA Change: V230A
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180
AA Change: V230A
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
18 |
59 |
4.06e-20 |
SMART |
|
ARID
|
81 |
170 |
4.76e-35 |
SMART |
|
BRIGHT
|
85 |
175 |
2.48e-31 |
SMART |
|
PHD
|
295 |
341 |
1.16e-14 |
SMART |
|
JmjC
|
437 |
603 |
1.47e-64 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000135802
AA Change: V230A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: V230A
| Domain | Start | End | E-Value | Type |
|---|
|
JmjN
|
18 |
59 |
1.7e-22 |
SMART |
|
ARID
|
81 |
170 |
3.6e-39 |
SMART |
|
BRIGHT
|
85 |
175 |
1.2e-33 |
SMART |
|
PHD
|
295 |
341 |
7.3e-17 |
SMART |
|
Blast:JmjC
|
384 |
436 |
2e-22 |
BLAST |
|
JmjC
|
437 |
603 |
2.2e-75 |
SMART |
|
low complexity region
|
638 |
651 |
N/A |
INTRINSIC |
|
Pfam:zf-C5HC2
|
676 |
728 |
6.3e-15 |
PFAM |
|
Pfam:PLU-1
|
741 |
811 |
9.8e-16 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000203373
AA Change: V63A
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000144720
Gene: ENSMUSG00000030180
AA Change: V63A
| Domain | Start | End | E-Value | Type |
|---|
|
BRIGHT
|
1 |
53 |
8.4e-4 |
SMART |
|
Blast:JmjC
|
58 |
153 |
3e-56 |
BLAST |
|
PDB:2E6R|A
|
121 |
152 |
4e-9 |
PDB |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.5%
- 20x: 95.9%
|
| Validation Efficiency |
100% (51/51) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene may play a role in tumor progression. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced body size, abnormal involuntary movement and quantitative changes in the hematopoietic stem cell and myeloid progenitor compartments, consistent with enhanced survival and increased cycling. Neonatalsurvival is sensitive to genetic background. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca5 |
A |
T |
11: 110,205,378 (GRCm39) |
L301Q |
probably damaging |
Het |
| Adgrl4 |
T |
C |
3: 151,223,443 (GRCm39) |
L632P |
probably damaging |
Het |
| Cacna2d1 |
T |
A |
5: 16,527,562 (GRCm39) |
I539N |
probably benign |
Het |
| Camta1 |
T |
A |
4: 151,164,306 (GRCm39) |
H314L |
probably damaging |
Het |
| Car2 |
T |
C |
3: 14,953,025 (GRCm39) |
S56P |
probably damaging |
Het |
| Chrm5 |
G |
A |
2: 112,309,793 (GRCm39) |
A441V |
probably damaging |
Het |
| Ckap5 |
T |
A |
2: 91,426,819 (GRCm39) |
N1380K |
possibly damaging |
Het |
| Cspg4 |
T |
C |
9: 56,799,976 (GRCm39) |
V1580A |
probably benign |
Het |
| Dcc |
A |
G |
18: 71,469,106 (GRCm39) |
L1099P |
probably damaging |
Het |
| Dnase1l1 |
C |
T |
X: 73,320,644 (GRCm39) |
|
probably null |
Homo |
| Epha5 |
A |
T |
5: 84,254,606 (GRCm39) |
H644Q |
probably damaging |
Het |
| Eya3 |
T |
C |
4: 132,400,221 (GRCm39) |
I80T |
probably damaging |
Het |
| Fdft1 |
A |
T |
14: 63,388,721 (GRCm39) |
Y304N |
probably damaging |
Het |
| Fiz1 |
C |
T |
7: 5,011,400 (GRCm39) |
A373T |
possibly damaging |
Het |
| Gpatch2l |
T |
A |
12: 86,307,379 (GRCm39) |
Y252* |
probably null |
Het |
| Hivep1 |
G |
T |
13: 42,313,147 (GRCm39) |
G1796* |
probably null |
Het |
| Irf8 |
T |
C |
8: 121,480,446 (GRCm39) |
V228A |
probably damaging |
Het |
| Islr |
A |
C |
9: 58,064,379 (GRCm39) |
V376G |
probably damaging |
Het |
| Lpgat1 |
A |
G |
1: 191,508,684 (GRCm39) |
|
probably null |
Het |
| Lrp8 |
T |
C |
4: 107,726,353 (GRCm39) |
|
probably null |
Het |
| Lyzl4 |
A |
C |
9: 121,407,150 (GRCm39) |
S127A |
possibly damaging |
Het |
| Map4k1 |
T |
C |
7: 28,699,715 (GRCm39) |
V606A |
possibly damaging |
Het |
| Mau2 |
T |
A |
8: 70,484,173 (GRCm39) |
K138N |
probably damaging |
Het |
| Meikin |
T |
C |
11: 54,261,592 (GRCm39) |
L33P |
probably damaging |
Het |
| Mrpl28 |
T |
C |
17: 26,345,252 (GRCm39) |
V224A |
probably benign |
Het |
| Ncdn |
T |
C |
4: 126,640,964 (GRCm39) |
D512G |
possibly damaging |
Het |
| Nlrp2 |
T |
A |
7: 5,303,925 (GRCm39) |
Q200L |
possibly damaging |
Het |
| Nup98 |
T |
C |
7: 101,843,957 (GRCm39) |
N89S |
possibly damaging |
Het |
| Ogfrl1 |
T |
G |
1: 23,408,944 (GRCm39) |
K427N |
probably benign |
Het |
| Or14a258 |
T |
A |
7: 86,035,059 (GRCm39) |
R270* |
probably null |
Het |
| Or52p2 |
A |
G |
7: 102,237,753 (GRCm39) |
C66R |
probably damaging |
Het |
| Or5b12 |
G |
T |
19: 12,896,946 (GRCm39) |
H242Q |
probably damaging |
Het |
| Or6c201 |
A |
T |
10: 128,969,535 (GRCm39) |
L34* |
probably null |
Het |
| Padi3 |
C |
T |
4: 140,530,819 (GRCm39) |
V68I |
possibly damaging |
Het |
| Pign |
A |
T |
1: 105,512,820 (GRCm39) |
M621K |
probably benign |
Het |
| Pigv |
C |
T |
4: 133,392,547 (GRCm39) |
V208M |
probably damaging |
Het |
| Ripk4 |
A |
G |
16: 97,564,726 (GRCm39) |
|
probably benign |
Het |
| Rsf1 |
A |
G |
7: 97,310,124 (GRCm39) |
K285E |
probably benign |
Het |
| Serpina3k |
G |
C |
12: 104,311,562 (GRCm39) |
G380A |
probably benign |
Het |
| Sorbs1 |
A |
G |
19: 40,365,426 (GRCm39) |
|
probably null |
Het |
| Srrd |
G |
C |
5: 112,487,866 (GRCm39) |
A104G |
probably benign |
Het |
| Tbp |
T |
A |
17: 15,721,351 (GRCm39) |
|
probably null |
Het |
| Tecrl |
G |
A |
5: 83,442,447 (GRCm39) |
H209Y |
probably damaging |
Het |
| Tmprss11c |
A |
G |
5: 86,404,204 (GRCm39) |
L157P |
probably damaging |
Het |
| Tmprss13 |
A |
T |
9: 45,254,498 (GRCm39) |
T422S |
possibly damaging |
Het |
| Ttll5 |
A |
G |
12: 86,003,473 (GRCm39) |
H1103R |
probably benign |
Het |
| Urb2 |
G |
T |
8: 124,757,864 (GRCm39) |
E1190D |
probably damaging |
Het |
| Vldlr |
A |
G |
19: 27,223,049 (GRCm39) |
Y699C |
probably damaging |
Het |
| Vmn1r22 |
T |
G |
6: 57,877,563 (GRCm39) |
N138T |
possibly damaging |
Het |
|
| Other mutations in Kdm5a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00540:Kdm5a
|
APN |
6 |
120,362,680 (GRCm39) |
critical splice donor site |
probably null |
0.00 |
|
IGL00706:Kdm5a
|
APN |
6 |
120,383,597 (GRCm39) |
missense |
possibly damaging |
0.44 |
|
IGL01361:Kdm5a
|
APN |
6 |
120,375,977 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01402:Kdm5a
|
APN |
6 |
120,367,640 (GRCm39) |
nonsense |
probably null |
0.00 |
|
IGL01924:Kdm5a
|
APN |
6 |
120,371,216 (GRCm39) |
critical splice donor site |
probably null |
0.00 |
|
IGL01935:Kdm5a
|
APN |
6 |
120,385,284 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL02165:Kdm5a
|
APN |
6 |
120,392,251 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02472:Kdm5a
|
APN |
6 |
120,383,691 (GRCm39) |
splice site |
probably benign |
|
|
IGL02506:Kdm5a
|
APN |
6 |
120,409,110 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02604:Kdm5a
|
APN |
6 |
120,408,941 (GRCm39) |
missense |
probably benign |
|
|
IGL02633:Kdm5a
|
APN |
6 |
120,341,680 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02876:Kdm5a
|
APN |
6 |
120,367,605 (GRCm39) |
unclassified |
probably benign |
|
|
IGL03009:Kdm5a
|
APN |
6 |
120,407,047 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL03027:Kdm5a
|
APN |
6 |
120,351,951 (GRCm39) |
splice site |
probably null |
|
|
IGL03164:Kdm5a
|
APN |
6 |
120,415,980 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03236:Kdm5a
|
APN |
6 |
120,415,949 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL03276:Kdm5a
|
APN |
6 |
120,379,669 (GRCm39) |
splice site |
probably benign |
|
|
Anastasia
|
UTSW |
6 |
120,407,192 (GRCm39) |
nonsense |
probably null |
|
|
Augmented
|
UTSW |
6 |
120,406,977 (GRCm39) |
intron |
probably benign |
|
|
Calla_lily
|
UTSW |
6 |
120,381,983 (GRCm39) |
missense |
probably damaging |
1.00 |
|
crocus
|
UTSW |
6 |
120,375,999 (GRCm39) |
missense |
probably null |
0.98 |
|
Magnolia
|
UTSW |
6 |
120,375,939 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Saffron
|
UTSW |
6 |
120,366,581 (GRCm39) |
missense |
probably benign |
0.19 |
|
Selbst
|
UTSW |
6 |
120,365,066 (GRCm39) |
nonsense |
probably null |
|
|
R0320:Kdm5a
|
UTSW |
6 |
120,366,581 (GRCm39) |
missense |
probably benign |
0.19 |
|
R0462:Kdm5a
|
UTSW |
6 |
120,379,561 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0601:Kdm5a
|
UTSW |
6 |
120,379,632 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
R0628:Kdm5a
|
UTSW |
6 |
120,392,200 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1024:Kdm5a
|
UTSW |
6 |
120,375,999 (GRCm39) |
missense |
probably null |
0.98 |
|
R2013:Kdm5a
|
UTSW |
6 |
120,408,951 (GRCm39) |
missense |
probably benign |
0.09 |
|
R2015:Kdm5a
|
UTSW |
6 |
120,408,951 (GRCm39) |
missense |
probably benign |
0.09 |
|
R2061:Kdm5a
|
UTSW |
6 |
120,358,578 (GRCm39) |
missense |
probably benign |
|
|
R2188:Kdm5a
|
UTSW |
6 |
120,383,601 (GRCm39) |
missense |
possibly damaging |
0.59 |
|
R3923:Kdm5a
|
UTSW |
6 |
120,358,625 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4013:Kdm5a
|
UTSW |
6 |
120,371,067 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4016:Kdm5a
|
UTSW |
6 |
120,371,067 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4017:Kdm5a
|
UTSW |
6 |
120,371,067 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4030:Kdm5a
|
UTSW |
6 |
120,382,074 (GRCm39) |
nonsense |
probably null |
|
|
R4646:Kdm5a
|
UTSW |
6 |
120,351,938 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
R4737:Kdm5a
|
UTSW |
6 |
120,382,976 (GRCm39) |
intron |
probably benign |
|
|
R4779:Kdm5a
|
UTSW |
6 |
120,346,060 (GRCm39) |
unclassified |
probably benign |
|
|
R4836:Kdm5a
|
UTSW |
6 |
120,389,363 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5129:Kdm5a
|
UTSW |
6 |
120,381,983 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5182:Kdm5a
|
UTSW |
6 |
120,365,066 (GRCm39) |
nonsense |
probably null |
|
|
R5183:Kdm5a
|
UTSW |
6 |
120,406,977 (GRCm39) |
intron |
probably benign |
|
|
R5572:Kdm5a
|
UTSW |
6 |
120,389,336 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R6110:Kdm5a
|
UTSW |
6 |
120,389,267 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6132:Kdm5a
|
UTSW |
6 |
120,351,892 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6198:Kdm5a
|
UTSW |
6 |
120,415,958 (GRCm39) |
missense |
probably benign |
0.37 |
|
R6246:Kdm5a
|
UTSW |
6 |
120,408,871 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R6336:Kdm5a
|
UTSW |
6 |
120,375,939 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6612:Kdm5a
|
UTSW |
6 |
120,407,189 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6647:Kdm5a
|
UTSW |
6 |
120,389,422 (GRCm39) |
missense |
probably benign |
0.25 |
|
R7068:Kdm5a
|
UTSW |
6 |
120,407,176 (GRCm39) |
missense |
probably benign |
0.40 |
|
R7369:Kdm5a
|
UTSW |
6 |
120,408,965 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R7380:Kdm5a
|
UTSW |
6 |
120,382,879 (GRCm39) |
missense |
probably benign |
0.35 |
|
R7411:Kdm5a
|
UTSW |
6 |
120,403,776 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7521:Kdm5a
|
UTSW |
6 |
120,409,148 (GRCm39) |
nonsense |
probably null |
|
|
R7570:Kdm5a
|
UTSW |
6 |
120,404,803 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7647:Kdm5a
|
UTSW |
6 |
120,404,747 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7704:Kdm5a
|
UTSW |
6 |
120,404,025 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7796:Kdm5a
|
UTSW |
6 |
120,367,724 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7875:Kdm5a
|
UTSW |
6 |
120,375,979 (GRCm39) |
nonsense |
probably null |
|
|
R8265:Kdm5a
|
UTSW |
6 |
120,383,557 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R8297:Kdm5a
|
UTSW |
6 |
120,358,516 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8336:Kdm5a
|
UTSW |
6 |
120,396,407 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8471:Kdm5a
|
UTSW |
6 |
120,407,192 (GRCm39) |
nonsense |
probably null |
|
|
R8872:Kdm5a
|
UTSW |
6 |
120,365,101 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8890:Kdm5a
|
UTSW |
6 |
120,366,624 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9028:Kdm5a
|
UTSW |
6 |
120,416,092 (GRCm39) |
missense |
probably benign |
|
|
R9064:Kdm5a
|
UTSW |
6 |
120,403,869 (GRCm39) |
small deletion |
probably benign |
|
|
R9114:Kdm5a
|
UTSW |
6 |
120,382,887 (GRCm39) |
nonsense |
probably null |
|
|
R9316:Kdm5a
|
UTSW |
6 |
120,381,973 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9353:Kdm5a
|
UTSW |
6 |
120,404,730 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9412:Kdm5a
|
UTSW |
6 |
120,365,991 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9416:Kdm5a
|
UTSW |
6 |
120,365,056 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9431:Kdm5a
|
UTSW |
6 |
120,392,253 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9711:Kdm5a
|
UTSW |
6 |
120,367,658 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GGAAAACTTCTGGTACCTAGGC -3'
(R):5'- GAATTCCCAGCATAGAGTGAAATTC -3'
Sequencing Primer
(F):5'- TTCTGGTACCTAGGCCCACAATAG -3'
(R):5'- TTCAAACATCACTTGAGCCTTG -3'
|
| Posted On |
2018-04-27 |
Incidental Mutation