Incidental Mutation 'R4285:Kdm1a'
| ID |
322022 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1a
|
| Ensembl Gene |
ENSMUSG00000036940 |
| Gene Name |
lysine (K)-specific demethylase 1A |
| Synonyms |
1810043O07Rik, Kdm1, LSD1, Aof2 |
| MMRRC Submission |
041080-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4285 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
136277851-136330034 bp(-) (GRCm39) |
| Type of Mutation |
splice site (4 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 136309347 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000101473
(fasta)
|
| 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 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 |
noncoding transcript
Transcript: ENSMUST00000118562
|
| 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 |
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.4%
|
| Validation Efficiency |
98% (42/43) |
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Agl |
G |
A |
3: 116,545,827 (GRCm39) |
S1323L |
possibly damaging |
Het |
| Ahnak |
T |
A |
19: 8,994,203 (GRCm39) |
C5162* |
probably null |
Het |
| Carmil3 |
GGACGA |
GGA |
14: 55,736,933 (GRCm39) |
|
probably benign |
Het |
| Cfap73 |
T |
C |
5: 120,770,654 (GRCm39) |
K39E |
possibly damaging |
Het |
| Coq6 |
C |
T |
12: 84,417,178 (GRCm39) |
|
probably benign |
Het |
| Dlc1 |
C |
T |
8: 37,041,282 (GRCm39) |
E1316K |
possibly damaging |
Het |
| Dscam |
A |
G |
16: 96,510,309 (GRCm39) |
|
probably null |
Het |
| Eya2 |
T |
A |
2: 165,566,700 (GRCm39) |
N250K |
probably benign |
Het |
| Fat4 |
A |
G |
3: 38,943,320 (GRCm39) |
I738V |
probably benign |
Het |
| Gria2 |
T |
G |
3: 80,614,969 (GRCm39) |
|
probably benign |
Het |
| Hnrnph3 |
A |
T |
10: 62,852,247 (GRCm39) |
D238E |
probably damaging |
Het |
| Il1rn |
T |
C |
2: 24,239,557 (GRCm39) |
L151P |
probably damaging |
Het |
| Kctd19 |
G |
A |
8: 106,109,581 (GRCm39) |
|
probably benign |
Het |
| Klk14 |
G |
A |
7: 43,341,501 (GRCm39) |
C51Y |
probably damaging |
Het |
| Lamc1 |
C |
A |
1: 153,110,298 (GRCm39) |
G1126W |
probably damaging |
Het |
| Magi3 |
C |
A |
3: 103,923,184 (GRCm39) |
G1178* |
probably null |
Het |
| Man2a2 |
T |
C |
7: 80,018,367 (GRCm39) |
D141G |
probably damaging |
Het |
| Map2k1 |
C |
A |
9: 64,119,925 (GRCm39) |
V127L |
probably damaging |
Het |
| Memo1 |
T |
C |
17: 74,562,293 (GRCm39) |
|
probably null |
Het |
| Mxd3 |
A |
G |
13: 55,477,167 (GRCm39) |
S31P |
probably benign |
Het |
| Myo5b |
G |
A |
18: 74,847,920 (GRCm39) |
E1053K |
probably benign |
Het |
| Nup50l |
T |
C |
6: 96,142,733 (GRCm39) |
T104A |
probably benign |
Het |
| Or2m12 |
A |
C |
16: 19,104,714 (GRCm39) |
F260V |
probably damaging |
Het |
| Or51a5 |
G |
T |
7: 102,771,867 (GRCm39) |
Y37* |
probably null |
Het |
| Pex5l |
A |
G |
3: 33,061,336 (GRCm39) |
I171T |
probably damaging |
Het |
| Plag1 |
A |
G |
4: 3,905,654 (GRCm39) |
V12A |
probably benign |
Het |
| Podn |
C |
A |
4: 107,878,893 (GRCm39) |
V180L |
possibly damaging |
Het |
| Prox2 |
T |
A |
12: 85,141,698 (GRCm39) |
R168S |
probably benign |
Het |
| Prss29 |
A |
G |
17: 25,541,231 (GRCm39) |
Y225C |
probably damaging |
Het |
| Rassf2 |
G |
A |
2: 131,847,314 (GRCm39) |
T97I |
probably benign |
Het |
| Samm50 |
T |
C |
15: 84,081,213 (GRCm39) |
V47A |
probably damaging |
Het |
| Shroom3 |
G |
T |
5: 93,090,945 (GRCm39) |
V1151F |
probably damaging |
Het |
| Slc20a2 |
G |
A |
8: 23,051,365 (GRCm39) |
R466Q |
probably benign |
Het |
| Slc25a51 |
C |
T |
4: 45,399,768 (GRCm39) |
V141M |
probably benign |
Het |
| St6galnac3 |
A |
C |
3: 152,912,360 (GRCm39) |
V161G |
probably benign |
Het |
| Unc5c |
T |
C |
3: 141,420,435 (GRCm39) |
I52T |
probably damaging |
Het |
| Vat1l |
A |
G |
8: 114,932,523 (GRCm39) |
E23G |
probably damaging |
Het |
| Vmn2r91 |
A |
G |
17: 18,356,030 (GRCm39) |
T566A |
probably benign |
Het |
| Wls |
A |
T |
3: 159,639,902 (GRCm39) |
H511L |
probably benign |
Het |
| Zfp644 |
G |
A |
5: 106,782,984 (GRCm39) |
T1130I |
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 |
|
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 |
|
|
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 |
|
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTGAGATCGGCCTGAGGACTTC -3'
(R):5'- TAATTCCCTGGGCCTTGGTTAC -3'
Sequencing Primer
(F):5'- ATCGGCCTGAGGACTTCAACAG -3'
(R):5'- CCTTGGTTACAGGAGGAGC -3'
|
| Posted On |
2015-06-20 |
Incidental Mutation