Incidental Mutation 'R3788:Kdm2a'
| ID |
272411 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm2a
|
| Ensembl Gene |
ENSMUSG00000054611 |
| Gene Name |
lysine (K)-specific demethylase 2A |
| Synonyms |
Fbxl11, lalina, Fbl7, 5530401A10Rik, Gm4560, Cxxc8, Jhdm1a |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.966)
|
| Stock # |
R3788 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
4366172-4448749 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 4401833 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Serine
at position 207
(C207S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000076698
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000047898]
[ENSMUST00000075856]
[ENSMUST00000116571]
[ENSMUST00000175959]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000047898
AA Change: C207S
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: C207S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
23 |
34 |
N/A |
INTRINSIC |
|
low complexity region
|
127 |
138 |
N/A |
INTRINSIC |
|
JmjC
|
148 |
316 |
1.52e-34 |
SMART |
|
low complexity region
|
416 |
433 |
N/A |
INTRINSIC |
|
PDB:2YU2|A
|
440 |
517 |
1e-35 |
PDB |
|
Pfam:zf-CXXC
|
563 |
609 |
7.5e-16 |
PFAM |
|
PHD
|
619 |
676 |
3.25e-4 |
SMART |
|
low complexity region
|
848 |
875 |
N/A |
INTRINSIC |
|
FBOX
|
892 |
932 |
1.58e-2 |
SMART |
|
low complexity region
|
987 |
998 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000075856
AA Change: C207S
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: C207S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
23 |
34 |
N/A |
INTRINSIC |
|
low complexity region
|
127 |
138 |
N/A |
INTRINSIC |
|
JmjC
|
148 |
316 |
1.52e-34 |
SMART |
|
low complexity region
|
416 |
433 |
N/A |
INTRINSIC |
|
PDB:2YU2|A
|
440 |
517 |
1e-35 |
PDB |
|
Pfam:zf-CXXC
|
563 |
609 |
7.5e-16 |
PFAM |
|
PHD
|
619 |
676 |
3.25e-4 |
SMART |
|
low complexity region
|
848 |
875 |
N/A |
INTRINSIC |
|
FBOX
|
892 |
932 |
1.58e-2 |
SMART |
|
low complexity region
|
987 |
998 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000116571
AA Change: C207S
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000139651
Gene: ENSMUSG00000054611
AA Change: C207S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
23 |
34 |
N/A |
INTRINSIC |
|
low complexity region
|
127 |
138 |
N/A |
INTRINSIC |
|
JmjC
|
148 |
316 |
5.9e-37 |
SMART |
|
low complexity region
|
416 |
433 |
N/A |
INTRINSIC |
|
PDB:2YU2|A
|
440 |
493 |
4e-21 |
PDB |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175682
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175777
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000175959
AA Change: C184S
PolyPhen 2
Score 0.731 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000135689
Gene: ENSMUSG00000054611
AA Change: C184S
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:2YU2|A
|
1 |
206 |
1e-140 |
PDB |
|
Blast:JmjC
|
7 |
79 |
8e-23 |
BLAST |
|
Blast:JmjC
|
125 |
206 |
3e-55 |
BLAST |
|
| Meta Mutation Damage Score |
0.8738 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.1%
|
| Validation Efficiency |
100% (61/61) |
| 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 F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains at least six highly degenerated leucine-rich repeats. This family member plays a role in epigenetic silencing. It nucleates at CpG islands and specifically demethylates both mono- and di-methylated lysine-36 of histone H3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
PHENOTYPE: Mice homozygous for a null allele show embryonic lethality, severe growth retardation, reduced neuron proliferation, increased neuron apoptosis, impaired neuron differentiation, small hearts, abnormal cardiac looping and, in some cases, incomplete embryonic turning and neural tube closure defects. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca4 |
T |
A |
3: 121,846,561 (GRCm39) |
V26E |
possibly damaging |
Het |
| Abhd16a |
A |
G |
17: 35,320,563 (GRCm39) |
N411S |
probably damaging |
Het |
| Akap13 |
G |
A |
7: 75,351,901 (GRCm39) |
|
probably null |
Het |
| Aph1b |
T |
C |
9: 66,701,348 (GRCm39) |
|
probably benign |
Het |
| Aspm |
C |
T |
1: 139,390,941 (GRCm39) |
T742I |
probably damaging |
Het |
| Bclaf3 |
A |
G |
X: 158,349,492 (GRCm39) |
H619R |
probably benign |
Het |
| Bltp2 |
T |
A |
11: 78,179,123 (GRCm39) |
|
probably null |
Het |
| Cemip |
A |
T |
7: 83,593,106 (GRCm39) |
L1199H |
probably damaging |
Het |
| Chd2 |
G |
A |
7: 73,096,878 (GRCm39) |
|
probably benign |
Het |
| Clnk |
A |
G |
5: 38,872,341 (GRCm39) |
Y310H |
probably damaging |
Het |
| Crmp1 |
A |
G |
5: 37,441,484 (GRCm39) |
D522G |
probably damaging |
Het |
| Cyth3 |
A |
G |
5: 143,622,298 (GRCm39) |
|
probably benign |
Het |
| Dcbld1 |
T |
A |
10: 52,195,754 (GRCm39) |
Y392N |
probably damaging |
Het |
| Flnc |
T |
C |
6: 29,454,056 (GRCm39) |
F1820L |
probably damaging |
Het |
| Galnt18 |
G |
A |
7: 111,119,322 (GRCm39) |
R385* |
probably null |
Het |
| Gpatch3 |
C |
A |
4: 133,302,479 (GRCm39) |
R137S |
possibly damaging |
Het |
| Gpc6 |
C |
T |
14: 117,861,878 (GRCm39) |
P265S |
probably damaging |
Het |
| Harbi1 |
T |
A |
2: 91,550,952 (GRCm39) |
D308E |
probably benign |
Het |
| Hdhd2 |
G |
A |
18: 77,042,883 (GRCm39) |
|
probably null |
Het |
| Hk1 |
T |
C |
10: 62,111,467 (GRCm39) |
K737E |
possibly damaging |
Het |
| Hnrnpr |
G |
A |
4: 136,063,624 (GRCm39) |
V345M |
probably damaging |
Het |
| Ift56 |
T |
A |
6: 38,380,459 (GRCm39) |
|
probably null |
Het |
| Kalrn |
T |
C |
16: 34,040,610 (GRCm39) |
H944R |
probably damaging |
Het |
| Kirrel1 |
C |
T |
3: 86,996,458 (GRCm39) |
M380I |
probably null |
Het |
| Krt75 |
C |
T |
15: 101,481,956 (GRCm39) |
G104D |
possibly damaging |
Het |
| Lnpk |
A |
T |
2: 74,352,607 (GRCm39) |
S358R |
probably benign |
Het |
| Map2 |
A |
G |
1: 66,456,022 (GRCm39) |
T1512A |
probably damaging |
Het |
| Marchf10 |
T |
A |
11: 105,287,905 (GRCm39) |
L132F |
probably damaging |
Het |
| Mfrp |
G |
A |
9: 44,016,754 (GRCm39) |
W65* |
probably null |
Het |
| Mgat5 |
A |
G |
1: 127,294,180 (GRCm39) |
D174G |
probably benign |
Het |
| Miga2 |
T |
A |
2: 30,261,237 (GRCm39) |
Y177* |
probably null |
Het |
| Mroh3 |
T |
C |
1: 136,113,213 (GRCm39) |
D747G |
probably damaging |
Het |
| Muc5b |
A |
G |
7: 141,417,571 (GRCm39) |
T3506A |
possibly damaging |
Het |
| Myo7b |
G |
T |
18: 32,107,165 (GRCm39) |
P1277T |
possibly damaging |
Het |
| Naaa |
C |
T |
5: 92,420,413 (GRCm39) |
|
probably null |
Het |
| Ndufs2 |
T |
C |
1: 171,062,889 (GRCm39) |
D410G |
possibly damaging |
Het |
| Or51a25 |
A |
G |
7: 102,372,694 (GRCm39) |
|
probably null |
Het |
| Or5p78 |
T |
A |
7: 108,212,280 (GRCm39) |
Y255* |
probably null |
Het |
| Or7e177 |
A |
G |
9: 20,211,666 (GRCm39) |
I58V |
probably benign |
Het |
| Or8g35 |
A |
G |
9: 39,381,365 (GRCm39) |
I219T |
probably benign |
Het |
| Osbp |
A |
T |
19: 11,956,285 (GRCm39) |
Y409F |
probably benign |
Het |
| Plxnb1 |
T |
A |
9: 108,938,355 (GRCm39) |
V1303D |
possibly damaging |
Het |
| Prkcg |
G |
A |
7: 3,362,263 (GRCm39) |
D246N |
probably damaging |
Het |
| Ranbp17 |
GCCTGGATACTGACC |
GCC |
11: 33,169,203 (GRCm39) |
|
probably benign |
Het |
| Sbf1 |
G |
A |
15: 89,183,731 (GRCm39) |
R1261* |
probably null |
Het |
| Scn4a |
T |
C |
11: 106,235,100 (GRCm39) |
N341S |
probably damaging |
Het |
| Sec61a2 |
C |
A |
2: 5,884,436 (GRCm39) |
|
probably null |
Het |
| Sgcd |
T |
A |
11: 47,246,032 (GRCm39) |
K57* |
probably null |
Het |
| Sinhcaf |
A |
G |
6: 148,827,617 (GRCm39) |
S134P |
possibly damaging |
Het |
| Slc12a5 |
T |
C |
2: 164,835,695 (GRCm39) |
L861P |
probably damaging |
Het |
| Slc6a16 |
A |
G |
7: 44,909,386 (GRCm39) |
D184G |
probably benign |
Het |
| Snx7 |
A |
G |
3: 117,632,639 (GRCm39) |
|
probably benign |
Het |
| Sptbn2 |
A |
G |
19: 4,795,950 (GRCm39) |
I1710V |
probably damaging |
Het |
| Sytl2 |
A |
T |
7: 90,025,289 (GRCm39) |
I426F |
probably benign |
Het |
| Tdp1 |
A |
G |
12: 99,858,011 (GRCm39) |
|
probably benign |
Het |
| Tmem232 |
C |
A |
17: 65,689,628 (GRCm39) |
D496Y |
possibly damaging |
Het |
| Tomm20l |
C |
T |
12: 71,158,516 (GRCm39) |
A58V |
possibly damaging |
Het |
| Ttn |
T |
C |
2: 76,775,618 (GRCm39) |
E1854G |
unknown |
Het |
| Ttn |
A |
G |
2: 76,804,552 (GRCm39) |
V240A |
probably benign |
Het |
| Vmn2r98 |
A |
T |
17: 19,300,887 (GRCm39) |
T630S |
probably benign |
Het |
| Xrcc1 |
G |
C |
7: 24,266,333 (GRCm39) |
A220P |
probably benign |
Het |
|
| Other mutations in Kdm2a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00334:Kdm2a
|
APN |
19 |
4,406,926 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
IGL00679:Kdm2a
|
APN |
19 |
4,376,869 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01104:Kdm2a
|
APN |
19 |
4,406,766 (GRCm39) |
splice site |
probably benign |
|
|
IGL01161:Kdm2a
|
APN |
19 |
4,369,279 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL01433:Kdm2a
|
APN |
19 |
4,392,888 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
IGL01456:Kdm2a
|
APN |
19 |
4,401,783 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01467:Kdm2a
|
APN |
19 |
4,374,435 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL01517:Kdm2a
|
APN |
19 |
4,412,089 (GRCm39) |
splice site |
probably benign |
|
|
IGL01528:Kdm2a
|
APN |
19 |
4,393,083 (GRCm39) |
missense |
probably benign |
0.18 |
|
IGL02504:Kdm2a
|
APN |
19 |
4,406,799 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
IGL02895:Kdm2a
|
APN |
19 |
4,412,930 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03109:Kdm2a
|
APN |
19 |
4,379,135 (GRCm39) |
missense |
probably benign |
0.04 |
|
IGL03171:Kdm2a
|
APN |
19 |
4,406,792 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03256:Kdm2a
|
APN |
19 |
4,395,538 (GRCm39) |
unclassified |
probably benign |
|
|
BB009:Kdm2a
|
UTSW |
19 |
4,369,184 (GRCm39) |
missense |
probably damaging |
0.98 |
|
BB019:Kdm2a
|
UTSW |
19 |
4,369,184 (GRCm39) |
missense |
probably damaging |
0.98 |
|
P0027:Kdm2a
|
UTSW |
19 |
4,393,273 (GRCm39) |
splice site |
probably benign |
|
|
PIT4382001:Kdm2a
|
UTSW |
19 |
4,393,201 (GRCm39) |
missense |
probably benign |
|
|
R0220:Kdm2a
|
UTSW |
19 |
4,374,947 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R0961:Kdm2a
|
UTSW |
19 |
4,379,219 (GRCm39) |
missense |
probably benign |
0.07 |
|
R1662:Kdm2a
|
UTSW |
19 |
4,378,240 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2023:Kdm2a
|
UTSW |
19 |
4,372,492 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2191:Kdm2a
|
UTSW |
19 |
4,406,959 (GRCm39) |
splice site |
probably null |
|
|
R2207:Kdm2a
|
UTSW |
19 |
4,412,898 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2351:Kdm2a
|
UTSW |
19 |
4,379,154 (GRCm39) |
missense |
probably benign |
0.02 |
|
R2406:Kdm2a
|
UTSW |
19 |
4,372,546 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2882:Kdm2a
|
UTSW |
19 |
4,381,212 (GRCm39) |
critical splice donor site |
probably null |
|
|
R3792:Kdm2a
|
UTSW |
19 |
4,374,540 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R3950:Kdm2a
|
UTSW |
19 |
4,393,260 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R4235:Kdm2a
|
UTSW |
19 |
4,372,549 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4377:Kdm2a
|
UTSW |
19 |
4,379,082 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4466:Kdm2a
|
UTSW |
19 |
4,370,328 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4766:Kdm2a
|
UTSW |
19 |
4,374,535 (GRCm39) |
unclassified |
probably benign |
|
|
R4824:Kdm2a
|
UTSW |
19 |
4,412,815 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4838:Kdm2a
|
UTSW |
19 |
4,375,054 (GRCm39) |
missense |
probably benign |
0.41 |
|
R5283:Kdm2a
|
UTSW |
19 |
4,381,297 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6366:Kdm2a
|
UTSW |
19 |
4,374,960 (GRCm39) |
missense |
probably benign |
0.15 |
|
R6368:Kdm2a
|
UTSW |
19 |
4,400,345 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6522:Kdm2a
|
UTSW |
19 |
4,374,854 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R6716:Kdm2a
|
UTSW |
19 |
4,379,130 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6757:Kdm2a
|
UTSW |
19 |
4,369,271 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6912:Kdm2a
|
UTSW |
19 |
4,372,529 (GRCm39) |
missense |
probably benign |
0.06 |
|
R6996:Kdm2a
|
UTSW |
19 |
4,395,669 (GRCm39) |
missense |
probably benign |
0.16 |
|
R7090:Kdm2a
|
UTSW |
19 |
4,369,169 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7497:Kdm2a
|
UTSW |
19 |
4,374,404 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7542:Kdm2a
|
UTSW |
19 |
4,383,858 (GRCm39) |
start gained |
probably benign |
|
|
R7932:Kdm2a
|
UTSW |
19 |
4,369,184 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8199:Kdm2a
|
UTSW |
19 |
4,439,054 (GRCm39) |
missense |
unknown |
|
|
R8263:Kdm2a
|
UTSW |
19 |
4,374,392 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R8446:Kdm2a
|
UTSW |
19 |
4,406,916 (GRCm39) |
nonsense |
probably null |
|
|
R9158:Kdm2a
|
UTSW |
19 |
4,374,715 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R9303:Kdm2a
|
UTSW |
19 |
4,395,606 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9314:Kdm2a
|
UTSW |
19 |
4,372,510 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9351:Kdm2a
|
UTSW |
19 |
4,393,141 (GRCm39) |
missense |
|
|
|
R9353:Kdm2a
|
UTSW |
19 |
4,393,141 (GRCm39) |
missense |
|
|
|
R9411:Kdm2a
|
UTSW |
19 |
4,412,835 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9456:Kdm2a
|
UTSW |
19 |
4,393,141 (GRCm39) |
missense |
|
|
|
R9616:Kdm2a
|
UTSW |
19 |
4,370,308 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9625:Kdm2a
|
UTSW |
19 |
4,393,141 (GRCm39) |
missense |
|
|
|
RF046:Kdm2a
|
UTSW |
19 |
4,374,535 (GRCm39) |
unclassified |
probably benign |
|
|
X0028:Kdm2a
|
UTSW |
19 |
4,398,774 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0028:Kdm2a
|
UTSW |
19 |
4,370,299 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGGTAGCCATCTACAATTCTCTTCAC -3'
(R):5'- AAGATATGGTGTGTCATGCCTG -3'
Sequencing Primer
(F):5'- CTTCACATAGAATGGATGATGTCTCC -3'
(R):5'- GCCTACTCTAGTAGCAAATTCAGG -3'
|
| Posted On |
2015-03-25 |
Incidental Mutation