Incidental Mutation 'IGL01356:Kdm1a'
| ID |
75531 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Kdm1a
|
| Ensembl Gene |
ENSMUSG00000036940 |
| Gene Name |
lysine (K)-specific demethylase 1A |
| Synonyms |
Aof2, 1810043O07Rik, Kdm1, LSD1 |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
IGL01356
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
4 |
| Chromosomal Location |
136550540-136602723 bp(-) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 136553891 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Histidine
at position 669
(R669H)
|
| 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: R498H
|
| SMART Domains |
Protein: ENSMUSP00000035457
Gene: ENSMUSG00000036940
AA Change: R498H
| 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 damaging
Transcript: ENSMUST00000105847
AA Change: R689H
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940
AA Change: R689H
| 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 damaging
Transcript: ENSMUST00000116273
AA Change: R669H
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940
AA Change: R669H
| 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 |
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 |
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000171424
|
| 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: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9130011E15Rik |
C |
T |
19: 45,966,303 |
C149Y |
possibly damaging |
Het |
| 9230113P08Rik |
T |
A |
9: 35,908,948 |
C33* |
probably null |
Het |
| AA474408 |
T |
C |
7: 110,060,982 |
|
probably benign |
Het |
| Acsl1 |
T |
C |
8: 46,511,463 |
|
probably null |
Het |
| Adck2 |
T |
C |
6: 39,583,920 |
V463A |
probably benign |
Het |
| B4galt4 |
T |
A |
16: 38,754,144 |
I224N |
probably damaging |
Het |
| Caprin1 |
T |
C |
2: 103,775,456 |
T396A |
probably benign |
Het |
| Cbx3 |
T |
C |
6: 51,475,301 |
V32A |
probably damaging |
Het |
| Chd1 |
A |
T |
17: 15,749,865 |
K960I |
probably damaging |
Het |
| Cldn4 |
A |
G |
5: 134,946,489 |
I86T |
probably benign |
Het |
| Cst12 |
A |
C |
2: 148,789,548 |
D50A |
probably damaging |
Het |
| Dock10 |
A |
G |
1: 80,523,742 |
Y1864H |
probably damaging |
Het |
| Dscaml1 |
G |
A |
9: 45,746,857 |
G1642E |
probably benign |
Het |
| Jakmip3 |
T |
C |
7: 139,017,612 |
L241P |
probably damaging |
Het |
| Lin54 |
G |
A |
5: 100,454,017 |
P455S |
probably damaging |
Het |
| Lrig1 |
G |
A |
6: 94,609,893 |
P601S |
probably damaging |
Het |
| Lrig1 |
A |
G |
6: 94,654,920 |
Y100H |
probably benign |
Het |
| Mtrf1 |
A |
G |
14: 79,423,425 |
D419G |
probably benign |
Het |
| Naca |
C |
T |
10: 128,041,715 |
|
probably benign |
Het |
| Naip1 |
A |
G |
13: 100,423,214 |
L1094P |
probably damaging |
Het |
| Nell2 |
A |
T |
15: 95,229,183 |
N770K |
probably damaging |
Het |
| Notch4 |
A |
G |
17: 34,581,026 |
H987R |
possibly damaging |
Het |
| Olfr437 |
T |
A |
6: 43,167,390 |
C111S |
probably damaging |
Het |
| Olfr487 |
T |
A |
7: 108,211,726 |
I268F |
probably benign |
Het |
| Olfr844 |
T |
A |
9: 19,318,942 |
M142K |
probably damaging |
Het |
| Plcg1 |
G |
T |
2: 160,753,893 |
G561W |
probably damaging |
Het |
| Ripor3 |
T |
A |
2: 167,993,575 |
M159L |
probably benign |
Het |
| Serpinb6a |
A |
G |
13: 33,925,417 |
S111P |
possibly damaging |
Het |
| Tas1r3 |
A |
T |
4: 155,861,327 |
H537Q |
probably benign |
Het |
| Tefm |
G |
A |
11: 80,137,997 |
R43* |
probably null |
Het |
| Tiam1 |
A |
G |
16: 89,837,788 |
V878A |
probably damaging |
Het |
| Vmn1r203 |
A |
G |
13: 22,524,777 |
S243G |
probably damaging |
Het |
| Vmn2r124 |
G |
T |
17: 18,073,471 |
V607L |
probably benign |
Het |
| Vps8 |
T |
G |
16: 21,517,357 |
|
probably null |
Het |
| Ythdf2 |
A |
T |
4: 132,205,350 |
D166E |
possibly damaging |
Het |
| Zan |
A |
G |
5: 137,436,432 |
V2203A |
unknown |
Het |
|
| Other mutations in Kdm1a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00796:Kdm1a
|
APN |
4 |
136554247 |
missense |
probably damaging |
1.00 |
|
IGL01106:Kdm1a
|
APN |
4 |
136572328 |
splice site |
probably benign |
|
|
IGL01886:Kdm1a
|
APN |
4 |
136561016 |
critical splice donor site |
probably null |
|
|
IGL02605:Kdm1a
|
APN |
4 |
136551037 |
unclassified |
probably benign |
|
|
IGL02885:Kdm1a
|
APN |
4 |
136552535 |
missense |
probably benign |
0.00 |
|
Seven_falls
|
UTSW |
4 |
136568600 |
nonsense |
probably null |
|
|
R0095:Kdm1a
|
UTSW |
4 |
136550894 |
missense |
probably benign |
0.09 |
|
R0532:Kdm1a
|
UTSW |
4 |
136561066 |
missense |
probably damaging |
1.00 |
|
R0553:Kdm1a
|
UTSW |
4 |
136555298 |
missense |
probably damaging |
1.00 |
|
R3625:Kdm1a
|
UTSW |
4 |
136561108 |
missense |
possibly damaging |
0.93 |
|
R4085:Kdm1a
|
UTSW |
4 |
136551962 |
nonsense |
probably null |
|
|
R4285:Kdm1a
|
UTSW |
4 |
136582036 |
splice site |
probably null |
|
|
R5118:Kdm1a
|
UTSW |
4 |
136557358 |
unclassified |
probably benign |
|
|
R5493:Kdm1a
|
UTSW |
4 |
136557421 |
frame shift |
probably null |
|
|
R5800:Kdm1a
|
UTSW |
4 |
136573070 |
splice site |
probably null |
|
|
R5945:Kdm1a
|
UTSW |
4 |
136568701 |
splice site |
probably null |
|
|
R6256:Kdm1a
|
UTSW |
4 |
136568600 |
nonsense |
probably null |
|
|
R6508:Kdm1a
|
UTSW |
4 |
136554310 |
missense |
probably damaging |
1.00 |
|
R7243:Kdm1a
|
UTSW |
4 |
136551954 |
missense |
probably damaging |
1.00 |
|
R7270:Kdm1a
|
UTSW |
4 |
136552527 |
missense |
probably damaging |
0.97 |
|
R7723:Kdm1a
|
UTSW |
4 |
136557749 |
missense |
probably benign |
0.06 |
|
R8391:Kdm1a
|
UTSW |
4 |
136553843 |
missense |
probably benign |
0.45 |
|
R8698:Kdm1a
|
UTSW |
4 |
136559207 |
missense |
probably benign |
0.00 |
|
R8840:Kdm1a
|
UTSW |
4 |
136560405 |
missense |
probably damaging |
1.00 |
|
R9146:Kdm1a
|
UTSW |
4 |
136602428 |
missense |
unknown |
|
|
R9778:Kdm1a
|
UTSW |
4 |
136552581 |
missense |
probably damaging |
0.98 |
|
X0066:Kdm1a
|
UTSW |
4 |
136559225 |
missense |
probably damaging |
0.98 |
|
| Posted On |
2013-10-07 |
Incidental Mutation