Incidental Mutation 'IGL01886:Kdm1a'
| ID |
179157 |
| 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 # |
IGL01886
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
4 |
| Chromosomal Location |
136277851-136330034 bp(-) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
A to G
at 136288327 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 null
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 null
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: ENSMUST00000147886
|
| Predicted Effect |
probably null
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 null
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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Akt1 |
C |
T |
12: 112,625,592 (GRCm39) |
V136M |
probably benign |
Het |
| Ankrd34c |
A |
T |
9: 89,612,318 (GRCm39) |
L8M |
possibly damaging |
Het |
| Anks6 |
C |
A |
4: 47,044,850 (GRCm39) |
W352L |
probably damaging |
Het |
| Arhgap12 |
A |
T |
18: 6,027,613 (GRCm39) |
N768K |
probably damaging |
Het |
| Clec7a |
A |
T |
6: 129,440,140 (GRCm39) |
|
probably benign |
Het |
| Cyp3a13 |
G |
A |
5: 137,897,082 (GRCm39) |
P411S |
probably damaging |
Het |
| Elavl2 |
A |
G |
4: 91,152,330 (GRCm39) |
V129A |
probably damaging |
Het |
| Ercc6 |
T |
A |
14: 32,291,537 (GRCm39) |
S994T |
possibly damaging |
Het |
| Esco1 |
T |
A |
18: 10,595,262 (GRCm39) |
K8I |
probably damaging |
Het |
| Esr1 |
T |
A |
10: 4,806,861 (GRCm39) |
I259K |
probably damaging |
Het |
| Filip1l |
A |
G |
16: 57,391,613 (GRCm39) |
I734V |
possibly damaging |
Het |
| Gm10717 |
C |
T |
9: 3,025,616 (GRCm39) |
S67L |
probably benign |
Het |
| Gm10718 |
A |
T |
9: 3,025,118 (GRCm39) |
Y194F |
probably benign |
Het |
| Gm21738 |
G |
A |
14: 19,416,979 (GRCm38) |
S144L |
probably benign |
Het |
| Grin3a |
T |
A |
4: 49,702,814 (GRCm39) |
I891F |
probably damaging |
Het |
| Kat7 |
T |
C |
11: 95,196,959 (GRCm39) |
T27A |
probably benign |
Het |
| Kifc5b |
T |
C |
17: 27,151,091 (GRCm39) |
V663A |
probably damaging |
Het |
| Lama1 |
T |
G |
17: 68,114,792 (GRCm39) |
S2314A |
probably benign |
Het |
| Lrrc69 |
C |
T |
4: 14,703,984 (GRCm39) |
V279I |
probably benign |
Het |
| Mast3 |
A |
T |
8: 71,234,783 (GRCm39) |
L774Q |
possibly damaging |
Het |
| Med27 |
C |
A |
2: 29,303,494 (GRCm39) |
P9Q |
probably damaging |
Het |
| Myo5a |
C |
A |
9: 75,076,372 (GRCm39) |
|
probably benign |
Het |
| Myoz1 |
T |
C |
14: 20,705,377 (GRCm39) |
K14E |
probably damaging |
Het |
| Neb |
T |
C |
2: 52,073,857 (GRCm39) |
|
probably benign |
Het |
| Nlrp1a |
T |
C |
11: 71,014,327 (GRCm39) |
T308A |
probably benign |
Het |
| Or1l4b |
A |
G |
2: 37,036,521 (GRCm39) |
Y99C |
probably damaging |
Het |
| Or8d2b |
G |
T |
9: 38,788,844 (GRCm39) |
C124F |
probably damaging |
Het |
| Orc1 |
T |
A |
4: 108,461,154 (GRCm39) |
|
probably null |
Het |
| Pnkp |
G |
A |
7: 44,511,631 (GRCm39) |
A76T |
probably damaging |
Het |
| Polr3h |
T |
C |
15: 81,801,591 (GRCm39) |
E95G |
probably damaging |
Het |
| Prpf40b |
T |
A |
15: 99,202,328 (GRCm39) |
M62K |
unknown |
Het |
| Prpf8 |
C |
A |
11: 75,386,570 (GRCm39) |
Q1075K |
probably benign |
Het |
| Ptprg |
A |
G |
14: 12,179,280 (GRCm38) |
K766E |
probably benign |
Het |
| Rabgap1l |
A |
T |
1: 160,169,612 (GRCm39) |
N778K |
probably damaging |
Het |
| Riok3 |
T |
A |
18: 12,272,442 (GRCm39) |
N204K |
probably damaging |
Het |
| Shank3 |
A |
G |
15: 89,415,866 (GRCm39) |
K650E |
probably damaging |
Het |
| Sim1 |
T |
A |
10: 50,860,411 (GRCm39) |
S758T |
probably damaging |
Het |
| Slu7 |
T |
G |
11: 43,330,087 (GRCm39) |
N171K |
probably damaging |
Het |
| Sp140l2 |
A |
G |
1: 85,231,907 (GRCm39) |
|
probably benign |
Het |
| Sult6b2 |
A |
G |
6: 142,735,852 (GRCm39) |
|
probably null |
Het |
| Taf6l |
C |
T |
19: 8,755,450 (GRCm39) |
|
probably null |
Het |
| Ubtfl1 |
G |
A |
9: 18,321,017 (GRCm39) |
V182M |
possibly damaging |
Het |
| Vmn2r129 |
C |
T |
4: 156,690,549 (GRCm39) |
|
noncoding transcript |
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 |
|
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 |
2014-05-07 |
Incidental Mutation