Incidental Mutation 'R5118:Kdm1a'
ID |
392729 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Kdm1a
|
Ensembl Gene |
ENSMUSG00000036940 |
Gene Name |
lysine (K)-specific demethylase 1A |
Synonyms |
1810043O07Rik, Kdm1, LSD1, Aof2 |
MMRRC Submission |
042706-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R5118 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
4 |
Chromosomal Location |
136277851-136330034 bp(-) (GRCm39) |
Type of Mutation |
unclassified |
DNA Base Change (assembly) |
A to G
at 136284669 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000105847]
[ENSMUST00000116273]
[ENSMUST00000168936]
|
AlphaFold |
Q6ZQ88 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000046846
|
SMART Domains |
Protein: ENSMUSP00000035457 Gene: ENSMUSG00000036940
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: ENSMUST00000105847
|
SMART Domains |
Protein: ENSMUSP00000101473 Gene: ENSMUSG00000036940
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: ENSMUST00000116273
|
SMART Domains |
Protein: ENSMUSP00000111977 Gene: ENSMUSG00000036940
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 |
unknown
Transcript: ENSMUST00000155354
AA Change: F225S
|
SMART Domains |
Protein: ENSMUSP00000114268 Gene: ENSMUSG00000036940 AA Change: F225S
Domain | Start | End | E-Value | Type |
Pfam:Amino_oxidase
|
3 |
250 |
2.9e-12 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000171424
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000170979
|
SMART Domains |
Protein: ENSMUSP00000131385 Gene: ENSMUSG00000036940
Domain | Start | End | E-Value | Type |
Pfam:SWIRM
|
1 |
77 |
2.5e-18 |
PFAM |
Pfam:Pyr_redox_2
|
70 |
142 |
1.1e-7 |
PFAM |
Pfam:AlaDh_PNT_C
|
85 |
195 |
7.8e-8 |
PFAM |
Pfam:FAD_binding_2
|
93 |
140 |
1.7e-6 |
PFAM |
Pfam:Pyr_redox
|
93 |
142 |
8.2e-7 |
PFAM |
Pfam:DAO
|
93 |
319 |
2.8e-9 |
PFAM |
Pfam:NAD_binding_8
|
96 |
160 |
9.8e-16 |
PFAM |
Pfam:Amino_oxidase
|
101 |
313 |
5.1e-32 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000168936
|
Meta Mutation Damage Score |
0.0898 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.4%
- 20x: 92.7%
|
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 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: 46 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
2700049A03Rik |
G |
T |
12: 71,211,320 (GRCm39) |
E685* |
probably null |
Het |
2700049A03Rik |
A |
T |
12: 71,211,321 (GRCm39) |
E685V |
possibly damaging |
Het |
Adamts2 |
A |
G |
11: 50,672,696 (GRCm39) |
E648G |
probably damaging |
Het |
Ankrd55 |
A |
G |
13: 112,492,473 (GRCm39) |
S187G |
probably benign |
Het |
Cd44 |
C |
A |
2: 102,695,715 (GRCm39) |
E52D |
probably damaging |
Het |
Col6a5 |
T |
A |
9: 105,814,204 (GRCm39) |
I603F |
unknown |
Het |
Dmxl2 |
C |
A |
9: 54,368,271 (GRCm39) |
R233L |
probably damaging |
Het |
Dop1a |
T |
C |
9: 86,388,312 (GRCm39) |
F429L |
probably damaging |
Het |
Epsti1 |
T |
G |
14: 78,224,122 (GRCm39) |
|
probably null |
Het |
Erfe |
G |
T |
1: 91,298,438 (GRCm39) |
|
probably null |
Het |
Galnt5 |
A |
G |
2: 57,905,015 (GRCm39) |
D526G |
probably damaging |
Het |
Gatd1 |
A |
T |
7: 140,986,719 (GRCm39) |
|
probably benign |
Het |
Gm1330 |
T |
C |
2: 148,844,906 (GRCm39) |
|
probably benign |
Het |
Gm6181 |
G |
A |
7: 52,405,364 (GRCm39) |
|
noncoding transcript |
Het |
Irak2 |
T |
A |
6: 113,642,772 (GRCm39) |
V68D |
probably benign |
Het |
Kidins220 |
C |
A |
12: 25,042,296 (GRCm39) |
Q198K |
probably damaging |
Het |
Lgr5 |
A |
G |
10: 115,288,244 (GRCm39) |
V728A |
possibly damaging |
Het |
Micall2 |
G |
A |
5: 139,702,202 (GRCm39) |
T347M |
probably damaging |
Het |
Mrap2 |
T |
C |
9: 87,064,756 (GRCm39) |
F166L |
possibly damaging |
Het |
Msh3 |
A |
T |
13: 92,445,942 (GRCm39) |
|
probably benign |
Het |
Mul1 |
T |
A |
4: 138,166,660 (GRCm39) |
L238Q |
probably damaging |
Het |
Nuak1 |
G |
T |
10: 84,210,848 (GRCm39) |
H413Q |
probably benign |
Het |
Or10j27 |
T |
C |
1: 172,958,484 (GRCm39) |
Q100R |
possibly damaging |
Het |
Pcnt |
C |
T |
10: 76,248,002 (GRCm39) |
A931T |
probably damaging |
Het |
Pramel20 |
T |
C |
4: 143,297,697 (GRCm39) |
L39P |
probably damaging |
Het |
Pramel34 |
T |
A |
5: 93,785,656 (GRCm39) |
D208V |
probably benign |
Het |
Psmb4 |
T |
C |
3: 94,792,253 (GRCm39) |
Y223C |
probably damaging |
Het |
Rbm15b |
G |
T |
9: 106,763,301 (GRCm39) |
A289E |
possibly damaging |
Het |
Reg3b |
T |
A |
6: 78,349,111 (GRCm39) |
V79E |
probably damaging |
Het |
Rsl1 |
A |
G |
13: 67,330,045 (GRCm39) |
I164M |
probably damaging |
Het |
Rtp1 |
T |
C |
16: 23,250,285 (GRCm39) |
F217L |
probably benign |
Het |
Sfmbt1 |
T |
C |
14: 30,512,727 (GRCm39) |
L360P |
probably damaging |
Het |
Sorbs2 |
T |
C |
8: 46,248,822 (GRCm39) |
V611A |
probably damaging |
Het |
Tenm4 |
T |
A |
7: 96,542,293 (GRCm39) |
D1935E |
probably damaging |
Het |
Tep1 |
T |
C |
14: 51,093,044 (GRCm39) |
|
probably null |
Het |
Tmppe |
T |
G |
9: 114,234,549 (GRCm39) |
S283A |
probably benign |
Het |
Tmtc1 |
A |
G |
6: 148,171,485 (GRCm39) |
|
probably benign |
Het |
Trp63 |
T |
C |
16: 25,707,760 (GRCm39) |
I552T |
unknown |
Het |
Tspan2 |
C |
A |
3: 102,657,151 (GRCm39) |
D45E |
probably benign |
Het |
Tut4 |
T |
A |
4: 108,377,489 (GRCm39) |
D966E |
possibly damaging |
Het |
Ubr1 |
T |
C |
2: 120,712,745 (GRCm39) |
E1396G |
probably benign |
Het |
Usp17lc |
A |
T |
7: 103,067,868 (GRCm39) |
T388S |
probably benign |
Het |
Wdr46 |
T |
C |
17: 34,167,811 (GRCm39) |
V508A |
possibly damaging |
Het |
Zfp462 |
T |
A |
4: 55,010,667 (GRCm39) |
Y878N |
probably damaging |
Het |
Zfp703 |
C |
T |
8: 27,469,233 (GRCm39) |
P299L |
probably damaging |
Het |
Zfp954 |
T |
A |
7: 7,118,714 (GRCm39) |
T277S |
probably benign |
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 |
|
R0095:Kdm1a
|
UTSW |
4 |
136,278,205 (GRCm39) |
missense |
probably benign |
0.09 |
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 |
|
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 |
|
Predicted Primers |
PCR Primer
(F):5'- CTCTACGGTAGAGCTGTAATAAAGAG -3'
(R):5'- TTGTAGACAGCTTCAGGAGGAG -3'
Sequencing Primer
(F):5'- AGAGATAAACAACATCATGGTAAGTG -3'
(R):5'- TTCAGGAGGAGATGGCATATGCTTAC -3'
|
Posted On |
2016-06-15 |