Incidental Mutation 'R0095:Kdm1a'
ID |
17158 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm1a
|
Ensembl Gene |
ENSMUSG00000036940 |
Gene Name |
lysine (K)-specific demethylase 1A |
Synonyms |
1810043O07Rik, Kdm1, LSD1, Aof2 |
MMRRC Submission |
038381-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R0095 (G1)
|
Quality Score |
|
Status
|
Validated
|
Chromosome |
4 |
Chromosomal Location |
136277851-136330034 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 136278205 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Arginine to Histidine
at position 839
(R839H)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000111977
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001116]
[ENSMUST00000063021]
[ENSMUST00000105847]
[ENSMUST00000105849]
[ENSMUST00000116273]
[ENSMUST00000168936]
[ENSMUST00000170102]
|
AlphaFold |
Q6ZQ88 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000001116
|
SMART Domains |
Protein: ENSMUSP00000001116 Gene: ENSMUSG00000001089
Domain | Start | End | E-Value | Type |
SCOP:d1fxkc_
|
96 |
233 |
4e-3 |
SMART |
coiled coil region
|
264 |
350 |
N/A |
INTRINSIC |
internal_repeat_1
|
569 |
638 |
9.92e-6 |
PROSPERO |
low complexity region
|
756 |
769 |
N/A |
INTRINSIC |
low complexity region
|
783 |
796 |
N/A |
INTRINSIC |
internal_repeat_1
|
986 |
1056 |
9.92e-6 |
PROSPERO |
|
Predicted Effect |
unknown
Transcript: ENSMUST00000046846
AA Change: R668H
|
SMART Domains |
Protein: ENSMUSP00000035457 Gene: ENSMUSG00000036940 AA Change: R668H
Domain | Start | End | E-Value | Type |
low complexity region
|
47 |
80 |
N/A |
INTRINSIC |
Pfam:SWIRM
|
85 |
173 |
1.1e-20 |
PFAM |
Pfam:AlaDh_PNT_C
|
181 |
297 |
8.4e-8 |
PFAM |
Pfam:FAD_binding_2
|
189 |
236 |
1.6e-6 |
PFAM |
Pfam:Pyr_redox
|
189 |
237 |
6.5e-7 |
PFAM |
Pfam:DAO
|
189 |
457 |
1.5e-9 |
PFAM |
Pfam:NAD_binding_8
|
192 |
256 |
9e-16 |
PFAM |
Pfam:Amino_oxidase
|
197 |
657 |
7e-133 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000063021
|
SMART Domains |
Protein: ENSMUSP00000060619 Gene: ENSMUSG00000001089
Domain | Start | End | E-Value | Type |
SCOP:d1fxkc_
|
96 |
233 |
4e-3 |
SMART |
coiled coil region
|
264 |
350 |
N/A |
INTRINSIC |
internal_repeat_1
|
569 |
638 |
9.92e-6 |
PROSPERO |
low complexity region
|
756 |
769 |
N/A |
INTRINSIC |
low complexity region
|
783 |
796 |
N/A |
INTRINSIC |
internal_repeat_1
|
986 |
1056 |
9.92e-6 |
PROSPERO |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000105847
AA Change: R859H
PolyPhen 2
Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)
|
SMART Domains |
Protein: ENSMUSP00000101473 Gene: ENSMUSG00000036940 AA Change: R859H
Domain | Start | End | E-Value | Type |
low complexity region
|
7 |
40 |
N/A |
INTRINSIC |
low complexity region
|
76 |
97 |
N/A |
INTRINSIC |
low complexity region
|
139 |
172 |
N/A |
INTRINSIC |
low complexity region
|
177 |
194 |
N/A |
INTRINSIC |
Pfam:SWIRM
|
197 |
285 |
8.8e-21 |
PFAM |
Pfam:FAD_binding_2
|
301 |
348 |
6e-6 |
PFAM |
Pfam:Pyr_redox
|
301 |
349 |
3e-6 |
PFAM |
Pfam:DAO
|
301 |
557 |
9.9e-9 |
PFAM |
Pfam:NAD_binding_8
|
304 |
368 |
4e-15 |
PFAM |
Pfam:Amino_oxidase
|
309 |
847 |
2e-133 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000105849
|
SMART Domains |
Protein: ENSMUSP00000101475 Gene: ENSMUSG00000001089
Domain | Start | End | E-Value | Type |
SCOP:d1fxkc_
|
96 |
233 |
4e-3 |
SMART |
coiled coil region
|
264 |
350 |
N/A |
INTRINSIC |
internal_repeat_1
|
569 |
638 |
9.92e-6 |
PROSPERO |
low complexity region
|
756 |
769 |
N/A |
INTRINSIC |
low complexity region
|
783 |
796 |
N/A |
INTRINSIC |
internal_repeat_1
|
986 |
1056 |
9.92e-6 |
PROSPERO |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000116273
AA Change: R839H
PolyPhen 2
Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)
|
SMART Domains |
Protein: ENSMUSP00000111977 Gene: ENSMUSG00000036940 AA Change: R839H
Domain | Start | End | E-Value | Type |
low complexity region
|
7 |
40 |
N/A |
INTRINSIC |
low complexity region
|
76 |
97 |
N/A |
INTRINSIC |
low complexity region
|
139 |
172 |
N/A |
INTRINSIC |
Pfam:SWIRM
|
175 |
265 |
2.7e-21 |
PFAM |
Pfam:Pyr_redox
|
281 |
327 |
5.5e-7 |
PFAM |
Pfam:FAD_binding_2
|
281 |
328 |
5.3e-6 |
PFAM |
Pfam:DAO
|
281 |
403 |
3.7e-8 |
PFAM |
Pfam:NAD_binding_8
|
284 |
348 |
5.7e-16 |
PFAM |
Pfam:Amino_oxidase
|
289 |
827 |
9.6e-166 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125111
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139690
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147886
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000171424
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000155354
|
SMART Domains |
Protein: ENSMUSP00000114268 Gene: ENSMUSG00000036940
Domain | Start | End | E-Value | Type |
Pfam:Amino_oxidase
|
3 |
250 |
2.9e-12 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000168936
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000170102
|
SMART Domains |
Protein: ENSMUSP00000130758 Gene: ENSMUSG00000001089
Domain | Start | End | E-Value | Type |
SCOP:d1fxkc_
|
96 |
233 |
4e-3 |
SMART |
coiled coil region
|
264 |
350 |
N/A |
INTRINSIC |
internal_repeat_1
|
569 |
638 |
9.92e-6 |
PROSPERO |
low complexity region
|
756 |
769 |
N/A |
INTRINSIC |
low complexity region
|
783 |
796 |
N/A |
INTRINSIC |
internal_repeat_1
|
986 |
1056 |
9.92e-6 |
PROSPERO |
|
Meta Mutation Damage Score |
0.3349 |
Coding Region Coverage |
- 1x: 88.6%
- 3x: 85.1%
- 10x: 74.3%
- 20x: 56.3%
|
Validation Efficiency |
88% (50/57) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009] PHENOTYPE: Homozygous disruption of this gene results in abnormal gastrulation and early embryonic lethality. Homozygotes lacking the neurospecific isoform are hypoexcitable and display decreased susceptibility to pharmacologically induced seizures. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 38 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adhfe1 |
T |
C |
1: 9,630,402 (GRCm39) |
I317T |
possibly damaging |
Het |
Aldh3a2 |
C |
T |
11: 61,141,774 (GRCm39) |
G21D |
probably damaging |
Het |
Alms1 |
C |
A |
6: 85,597,235 (GRCm39) |
T1156N |
possibly damaging |
Het |
Anxa8 |
G |
A |
14: 33,808,028 (GRCm39) |
A6T |
probably benign |
Het |
Arhgef4 |
C |
T |
1: 34,771,451 (GRCm39) |
Q86* |
probably null |
Het |
Atp4a |
T |
A |
7: 30,420,160 (GRCm39) |
I769N |
probably damaging |
Het |
Cacnb2 |
G |
T |
2: 14,963,586 (GRCm39) |
V61F |
probably damaging |
Het |
Clcf1 |
T |
G |
19: 4,265,842 (GRCm39) |
|
probably benign |
Het |
Cmah |
G |
T |
13: 24,620,668 (GRCm39) |
A301S |
probably benign |
Het |
Col6a4 |
A |
G |
9: 105,952,555 (GRCm39) |
W448R |
probably benign |
Het |
Csmd1 |
A |
T |
8: 16,283,065 (GRCm39) |
D630E |
probably damaging |
Het |
Dock10 |
A |
T |
1: 80,501,788 (GRCm39) |
Y1434N |
probably benign |
Het |
Etl4 |
A |
G |
2: 20,748,679 (GRCm39) |
D137G |
probably damaging |
Het |
Fer |
A |
T |
17: 64,248,321 (GRCm39) |
E361V |
possibly damaging |
Het |
Foxp2 |
C |
A |
6: 15,196,976 (GRCm39) |
A6E |
probably damaging |
Het |
Gpr3 |
T |
A |
4: 132,938,597 (GRCm39) |
D25V |
probably benign |
Het |
Gstm7 |
A |
T |
3: 107,837,879 (GRCm39) |
|
probably benign |
Het |
Gys1 |
T |
C |
7: 45,094,073 (GRCm39) |
V332A |
possibly damaging |
Het |
Igsf10 |
A |
T |
3: 59,238,617 (GRCm39) |
Y521* |
probably null |
Het |
Itk |
T |
C |
11: 46,233,279 (GRCm39) |
D266G |
probably damaging |
Het |
Lypla1 |
T |
C |
1: 4,900,550 (GRCm39) |
|
probably benign |
Het |
Mmp1a |
G |
A |
9: 7,465,621 (GRCm39) |
G186D |
possibly damaging |
Het |
Myl3 |
A |
C |
9: 110,596,997 (GRCm39) |
D119A |
probably damaging |
Het |
Necab1 |
T |
A |
4: 14,960,027 (GRCm39) |
N307Y |
possibly damaging |
Het |
Or5p81 |
A |
C |
7: 108,267,252 (GRCm39) |
I210L |
probably benign |
Het |
Plekha5 |
T |
C |
6: 140,474,323 (GRCm39) |
F84L |
probably damaging |
Het |
Plxnb2 |
A |
G |
15: 89,049,534 (GRCm39) |
S562P |
probably benign |
Het |
Rfx8 |
C |
T |
1: 39,724,696 (GRCm39) |
V222M |
possibly damaging |
Het |
Rpap3 |
A |
G |
15: 97,578,417 (GRCm39) |
|
probably benign |
Het |
Rpl6 |
T |
G |
5: 121,343,902 (GRCm39) |
V115G |
possibly damaging |
Het |
Sec16a |
A |
T |
2: 26,315,772 (GRCm39) |
|
probably null |
Het |
Sema3d |
T |
C |
5: 12,613,314 (GRCm39) |
Y464H |
probably damaging |
Het |
Sgo2a |
T |
A |
1: 58,054,714 (GRCm39) |
N299K |
probably benign |
Het |
Tecrl |
T |
C |
5: 83,442,417 (GRCm39) |
|
probably benign |
Het |
Thsd7a |
T |
C |
6: 12,320,969 (GRCm39) |
T1569A |
probably damaging |
Het |
U2surp |
T |
C |
9: 95,382,737 (GRCm39) |
|
probably null |
Het |
Unc45a |
T |
C |
7: 79,979,291 (GRCm39) |
D567G |
probably damaging |
Het |
Zfp532 |
A |
G |
18: 65,757,855 (GRCm39) |
Y596C |
probably damaging |
Het |
|
Other mutations in Kdm1a |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00796:Kdm1a
|
APN |
4 |
136,281,558 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01106:Kdm1a
|
APN |
4 |
136,299,639 (GRCm39) |
splice site |
probably benign |
|
IGL01356:Kdm1a
|
APN |
4 |
136,281,202 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01886:Kdm1a
|
APN |
4 |
136,288,327 (GRCm39) |
critical splice donor site |
probably null |
|
IGL02605:Kdm1a
|
APN |
4 |
136,278,348 (GRCm39) |
unclassified |
probably benign |
|
IGL02885:Kdm1a
|
APN |
4 |
136,279,846 (GRCm39) |
missense |
probably benign |
0.00 |
Seven_falls
|
UTSW |
4 |
136,295,911 (GRCm39) |
nonsense |
probably null |
|
R0532:Kdm1a
|
UTSW |
4 |
136,288,377 (GRCm39) |
missense |
probably damaging |
1.00 |
R0553:Kdm1a
|
UTSW |
4 |
136,282,609 (GRCm39) |
missense |
probably damaging |
1.00 |
R3625:Kdm1a
|
UTSW |
4 |
136,288,419 (GRCm39) |
missense |
possibly damaging |
0.93 |
R4085:Kdm1a
|
UTSW |
4 |
136,279,273 (GRCm39) |
nonsense |
probably null |
|
R4285:Kdm1a
|
UTSW |
4 |
136,309,347 (GRCm39) |
splice site |
probably null |
|
R5118:Kdm1a
|
UTSW |
4 |
136,284,669 (GRCm39) |
unclassified |
probably benign |
|
R5493:Kdm1a
|
UTSW |
4 |
136,284,732 (GRCm39) |
frame shift |
probably null |
|
R5800:Kdm1a
|
UTSW |
4 |
136,300,381 (GRCm39) |
splice site |
probably null |
|
R5945:Kdm1a
|
UTSW |
4 |
136,296,012 (GRCm39) |
splice site |
probably null |
|
R6256:Kdm1a
|
UTSW |
4 |
136,295,911 (GRCm39) |
nonsense |
probably null |
|
R6508:Kdm1a
|
UTSW |
4 |
136,281,621 (GRCm39) |
missense |
probably damaging |
1.00 |
R7243:Kdm1a
|
UTSW |
4 |
136,279,265 (GRCm39) |
missense |
probably damaging |
1.00 |
R7270:Kdm1a
|
UTSW |
4 |
136,279,838 (GRCm39) |
missense |
probably damaging |
0.97 |
R7723:Kdm1a
|
UTSW |
4 |
136,285,060 (GRCm39) |
missense |
probably benign |
0.06 |
R8391:Kdm1a
|
UTSW |
4 |
136,281,154 (GRCm39) |
missense |
probably benign |
0.45 |
R8698:Kdm1a
|
UTSW |
4 |
136,286,518 (GRCm39) |
missense |
probably benign |
0.00 |
R8840:Kdm1a
|
UTSW |
4 |
136,287,716 (GRCm39) |
missense |
probably damaging |
1.00 |
R9146:Kdm1a
|
UTSW |
4 |
136,329,739 (GRCm39) |
missense |
unknown |
|
R9778:Kdm1a
|
UTSW |
4 |
136,279,892 (GRCm39) |
missense |
probably damaging |
0.98 |
X0066:Kdm1a
|
UTSW |
4 |
136,286,536 (GRCm39) |
missense |
probably damaging |
0.98 |
|
Posted On |
2013-01-20 |