Incidental Mutation 'IGL01106:Kdm1a'
ID |
50904 |
Institutional Source |
Australian Phenomics Network
(link to record)
|
Gene Symbol |
Kdm1a
|
Ensembl Gene |
ENSMUSG00000036940 |
Gene Name |
lysine (K)-specific demethylase 1A |
Synonyms |
1810043O07Rik, Kdm1, LSD1, Aof2 |
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
IGL01106
|
Quality Score |
|
Status
|
|
Chromosome |
4 |
Chromosomal Location |
136277851-136330034 bp(-) (GRCm39) |
Type of Mutation |
splice site |
DNA Base Change (assembly) |
A to G
at 136299639 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000105847]
[ENSMUST00000116273]
|
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 |
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: 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 |
|
Coding Region Coverage |
|
Validation Efficiency |
|
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: 29 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Atg13 |
T |
C |
2: 91,526,297 (GRCm39) |
D12G |
probably damaging |
Het |
Cmya5 |
A |
G |
13: 93,221,120 (GRCm39) |
L3163P |
probably damaging |
Het |
Cntn2 |
A |
G |
1: 132,449,622 (GRCm39) |
|
probably benign |
Het |
Ddx23 |
C |
T |
15: 98,548,821 (GRCm39) |
R327Q |
probably benign |
Het |
Dlec1 |
G |
A |
9: 118,931,853 (GRCm39) |
E91K |
probably benign |
Het |
Fam13c |
T |
C |
10: 70,284,646 (GRCm39) |
|
probably null |
Het |
Fbn1 |
T |
C |
2: 125,193,626 (GRCm39) |
T1398A |
possibly damaging |
Het |
Frem1 |
T |
C |
4: 82,840,494 (GRCm39) |
T1793A |
probably benign |
Het |
Gprc5b |
T |
C |
7: 118,583,084 (GRCm39) |
K262E |
probably benign |
Het |
Hadh |
A |
T |
3: 131,034,619 (GRCm39) |
Y226N |
possibly damaging |
Het |
Herc1 |
T |
A |
9: 66,383,720 (GRCm39) |
|
probably benign |
Het |
Ikbke |
A |
G |
1: 131,187,792 (GRCm39) |
|
probably benign |
Het |
Iqcg |
T |
A |
16: 32,855,970 (GRCm39) |
I202L |
possibly damaging |
Het |
Kank3 |
G |
A |
17: 34,036,375 (GRCm39) |
G81E |
probably damaging |
Het |
Kcna3 |
A |
G |
3: 106,945,180 (GRCm39) |
E481G |
possibly damaging |
Het |
Klhdc8a |
A |
T |
1: 132,232,438 (GRCm39) |
S321C |
probably benign |
Het |
Kntc1 |
A |
G |
5: 123,900,666 (GRCm39) |
K255E |
probably benign |
Het |
Lhfpl4 |
T |
A |
6: 113,170,824 (GRCm39) |
T121S |
probably benign |
Het |
Lsm11 |
G |
A |
11: 45,824,490 (GRCm39) |
Q346* |
probably null |
Het |
Mcoln3 |
A |
G |
3: 145,843,019 (GRCm39) |
T368A |
probably benign |
Het |
Nlrp4g |
A |
T |
9: 124,350,452 (GRCm38) |
|
noncoding transcript |
Het |
Nol8 |
A |
G |
13: 49,807,957 (GRCm39) |
I58V |
possibly damaging |
Het |
Or5al6 |
C |
T |
2: 85,976,560 (GRCm39) |
V173M |
probably benign |
Het |
Phactr4 |
A |
G |
4: 132,098,116 (GRCm39) |
F384S |
probably benign |
Het |
Prkg1 |
T |
A |
19: 30,562,678 (GRCm39) |
I509L |
probably benign |
Het |
Rims1 |
T |
A |
1: 22,449,671 (GRCm39) |
D1019V |
probably damaging |
Het |
Sclt1 |
T |
C |
3: 41,629,754 (GRCm39) |
|
probably benign |
Het |
Sntg2 |
T |
A |
12: 30,307,987 (GRCm39) |
K233* |
probably null |
Het |
Syt5 |
T |
C |
7: 4,544,156 (GRCm39) |
T295A |
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 |
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 |
|
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 |
2013-06-21 |