Incidental Mutation 'IGL02885:Kdm1a'
| ID |
362984 |
| 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 # |
IGL02885
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
4 |
| Chromosomal Location |
136277851-136330034 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 136279846 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 719
(I719V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000111977
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001116]
[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: I548V
|
| SMART Domains |
Protein: ENSMUSP00000035457
Gene: ENSMUSG00000036940
AA Change: I548V
| 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
AA Change: I739V
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940
AA Change: I739V
| 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: I719V
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940
AA Change: I719V
| 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: ENSMUST00000168936
|
| 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: 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 |
|
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930407I10Rik |
A |
G |
15: 81,948,152 (GRCm39) |
N683S |
probably benign |
Het |
| Ahi1 |
T |
A |
10: 20,931,012 (GRCm39) |
F46I |
possibly damaging |
Het |
| Als2 |
C |
T |
1: 59,206,650 (GRCm39) |
V1598I |
probably benign |
Het |
| Arid1b |
A |
T |
17: 5,392,428 (GRCm39) |
D1986V |
probably damaging |
Het |
| Bhlhe41 |
T |
A |
6: 145,810,989 (GRCm39) |
D2V |
probably damaging |
Het |
| Borcs6 |
A |
G |
11: 68,951,072 (GRCm39) |
D150G |
possibly damaging |
Het |
| Ccdc88a |
G |
T |
11: 29,398,050 (GRCm39) |
R261L |
probably damaging |
Het |
| Ccne2 |
T |
A |
4: 11,198,723 (GRCm39) |
|
probably benign |
Het |
| Cenpk |
A |
G |
13: 104,385,903 (GRCm39) |
D266G |
probably damaging |
Het |
| Ces2b |
T |
C |
8: 105,561,563 (GRCm39) |
V219A |
probably damaging |
Het |
| Cpa1 |
A |
G |
6: 30,645,169 (GRCm39) |
R382G |
probably damaging |
Het |
| Cplx4 |
G |
T |
18: 66,089,984 (GRCm39) |
T145N |
probably damaging |
Het |
| Cyp19a1 |
T |
C |
9: 54,079,102 (GRCm39) |
I269V |
probably benign |
Het |
| Dennd3 |
A |
G |
15: 73,440,545 (GRCm39) |
Y1192C |
probably benign |
Het |
| Dpp6 |
T |
C |
5: 27,923,471 (GRCm39) |
Y694H |
probably damaging |
Het |
| Eea1 |
C |
A |
10: 95,877,346 (GRCm39) |
N1353K |
probably benign |
Het |
| Fam111a |
T |
A |
19: 12,561,488 (GRCm39) |
|
probably null |
Het |
| Fat1 |
T |
C |
8: 45,442,204 (GRCm39) |
S1169P |
probably benign |
Het |
| Frk |
G |
T |
10: 34,360,067 (GRCm39) |
A23S |
probably benign |
Het |
| Fyb2 |
T |
C |
4: 104,861,118 (GRCm39) |
V594A |
probably damaging |
Het |
| Gtpbp3 |
C |
A |
8: 71,942,064 (GRCm39) |
|
probably benign |
Het |
| Hoxa5 |
G |
T |
6: 52,179,688 (GRCm39) |
A229D |
probably damaging |
Het |
| Ift25 |
G |
A |
4: 107,130,866 (GRCm39) |
C52Y |
possibly damaging |
Het |
| Igf2r |
A |
T |
17: 12,913,007 (GRCm39) |
F1780L |
possibly damaging |
Het |
| Jade2 |
A |
T |
11: 51,722,123 (GRCm39) |
D143E |
probably damaging |
Het |
| Lama1 |
G |
A |
17: 68,111,531 (GRCm39) |
G2261R |
probably damaging |
Het |
| Lmx1b |
G |
T |
2: 33,457,216 (GRCm39) |
Q206K |
probably benign |
Het |
| Lrrtm4 |
G |
A |
6: 79,998,786 (GRCm39) |
G66D |
probably damaging |
Het |
| Myg1 |
G |
T |
15: 102,240,594 (GRCm39) |
G90C |
probably damaging |
Het |
| Nbea |
C |
T |
3: 55,539,407 (GRCm39) |
V2785I |
probably benign |
Het |
| Ncr1 |
C |
A |
7: 4,341,225 (GRCm39) |
P35Q |
probably damaging |
Het |
| Nos1 |
T |
A |
5: 118,033,855 (GRCm39) |
C326S |
probably damaging |
Het |
| Or12j2 |
T |
C |
7: 139,916,072 (GRCm39) |
F99S |
possibly damaging |
Het |
| Or3a1 |
G |
T |
11: 74,225,519 (GRCm39) |
H179Q |
possibly damaging |
Het |
| Or52r1 |
A |
T |
7: 102,537,243 (GRCm39) |
V39E |
possibly damaging |
Het |
| Pde4d |
A |
G |
13: 110,084,795 (GRCm39) |
Y520C |
probably damaging |
Het |
| Ppm1d |
A |
G |
11: 85,217,770 (GRCm39) |
M178V |
possibly damaging |
Het |
| Samd3 |
G |
A |
10: 26,147,762 (GRCm39) |
R479K |
probably benign |
Het |
| Semp2l2b |
T |
A |
10: 21,943,057 (GRCm39) |
I308F |
possibly damaging |
Het |
| Serpinb6a |
A |
G |
13: 34,102,782 (GRCm39) |
V226A |
probably benign |
Het |
| Slc26a4 |
T |
C |
12: 31,575,475 (GRCm39) |
E737G |
probably benign |
Het |
| Slc34a3 |
A |
G |
2: 25,121,069 (GRCm39) |
C340R |
probably damaging |
Het |
| Spata31d1b |
C |
A |
13: 59,866,941 (GRCm39) |
|
probably benign |
Het |
| Trappc12 |
A |
G |
12: 28,797,013 (GRCm39) |
V173A |
probably benign |
Het |
| Vmn2r66 |
A |
T |
7: 84,644,723 (GRCm39) |
D562E |
probably benign |
Het |
| Zfp395 |
C |
T |
14: 65,633,344 (GRCm39) |
P451L |
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 |
|
|
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 |
2015-12-18 |
Incidental Mutation