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 |
1810043O07Rik, Kdm1, LSD1, Aof2 |
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
IGL01356
|
Quality Score |
|
Status
|
|
Chromosome |
4 |
Chromosomal Location |
136277851-136330034 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 136281202 bp (GRCm39)
|
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]
[ENSMUST00000170102]
[ENSMUST00000168936]
|
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: ENSMUST00000147886
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139690
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000171424
|
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 |
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
|
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 |
AA474408 |
T |
C |
7: 109,660,189 (GRCm39) |
|
probably benign |
Het |
Acsl1 |
T |
C |
8: 46,964,500 (GRCm39) |
|
probably null |
Het |
Adck2 |
T |
C |
6: 39,560,854 (GRCm39) |
V463A |
probably benign |
Het |
Armh3 |
C |
T |
19: 45,954,742 (GRCm39) |
C149Y |
possibly damaging |
Het |
B4galt4 |
T |
A |
16: 38,574,506 (GRCm39) |
I224N |
probably damaging |
Het |
Caprin1 |
T |
C |
2: 103,605,801 (GRCm39) |
T396A |
probably benign |
Het |
Cbx3 |
T |
C |
6: 51,452,281 (GRCm39) |
V32A |
probably damaging |
Het |
Chd1 |
A |
T |
17: 15,970,127 (GRCm39) |
K960I |
probably damaging |
Het |
Cldn4 |
A |
G |
5: 134,975,343 (GRCm39) |
I86T |
probably benign |
Het |
Cst12 |
A |
C |
2: 148,631,468 (GRCm39) |
D50A |
probably damaging |
Het |
Dock10 |
A |
G |
1: 80,501,459 (GRCm39) |
Y1864H |
probably damaging |
Het |
Dscaml1 |
G |
A |
9: 45,658,155 (GRCm39) |
G1642E |
probably benign |
Het |
Jakmip3 |
T |
C |
7: 138,619,341 (GRCm39) |
L241P |
probably damaging |
Het |
Lin54 |
G |
A |
5: 100,601,876 (GRCm39) |
P455S |
probably damaging |
Het |
Lrig1 |
A |
G |
6: 94,631,901 (GRCm39) |
Y100H |
probably benign |
Het |
Lrig1 |
G |
A |
6: 94,586,874 (GRCm39) |
P601S |
probably damaging |
Het |
Mtrf1 |
A |
G |
14: 79,660,865 (GRCm39) |
D419G |
probably benign |
Het |
Naca |
C |
T |
10: 127,877,584 (GRCm39) |
|
probably benign |
Het |
Naip1 |
A |
G |
13: 100,559,722 (GRCm39) |
L1094P |
probably damaging |
Het |
Nell2 |
A |
T |
15: 95,127,064 (GRCm39) |
N770K |
probably damaging |
Het |
Notch4 |
A |
G |
17: 34,800,000 (GRCm39) |
H987R |
possibly damaging |
Het |
Or2a52 |
T |
A |
6: 43,144,324 (GRCm39) |
C111S |
probably damaging |
Het |
Or5p63 |
T |
A |
7: 107,810,933 (GRCm39) |
I268F |
probably benign |
Het |
Or7g26 |
T |
A |
9: 19,230,238 (GRCm39) |
M142K |
probably damaging |
Het |
Pate13 |
T |
A |
9: 35,820,244 (GRCm39) |
C33* |
probably null |
Het |
Plcg1 |
G |
T |
2: 160,595,813 (GRCm39) |
G561W |
probably damaging |
Het |
Ripor3 |
T |
A |
2: 167,835,495 (GRCm39) |
M159L |
probably benign |
Het |
Serpinb6a |
A |
G |
13: 34,109,400 (GRCm39) |
S111P |
possibly damaging |
Het |
Tas1r3 |
A |
T |
4: 155,945,784 (GRCm39) |
H537Q |
probably benign |
Het |
Tefm |
G |
A |
11: 80,028,823 (GRCm39) |
R43* |
probably null |
Het |
Tiam1 |
A |
G |
16: 89,634,676 (GRCm39) |
V878A |
probably damaging |
Het |
Vmn1r203 |
A |
G |
13: 22,708,947 (GRCm39) |
S243G |
probably damaging |
Het |
Vmn2r124 |
G |
T |
17: 18,293,733 (GRCm39) |
V607L |
probably benign |
Het |
Vps8 |
T |
G |
16: 21,336,107 (GRCm39) |
|
probably null |
Het |
Ythdf2 |
A |
T |
4: 131,932,661 (GRCm39) |
D166E |
possibly damaging |
Het |
Zan |
A |
G |
5: 137,434,694 (GRCm39) |
V2203A |
unknown |
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 |
|
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 |
2013-10-07 |