Incidental Mutation 'R9778:Kdm1a'
| ID |
733828 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Kdm1a
|
| Ensembl Gene |
ENSMUSG00000036940 |
| Gene Name |
lysine (K)-specific demethylase 1A |
| Synonyms |
1810043O07Rik, Kdm1, LSD1, Aof2 |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R9778 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
4 |
| Chromosomal Location |
136277851-136330034 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 136279892 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Methionine
at position 703
(I703M)
|
| 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 |
|
| SMART Domains |
Protein: ENSMUSP00000035457
Gene: ENSMUSG00000036940
AA Change: I532M
| 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 |
possibly damaging
Transcript: ENSMUST00000105847
AA Change: I723M
PolyPhen 2
Score 0.874 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940
AA Change: I723M
| 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: I703M
PolyPhen 2
Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940
AA Change: I703M
| 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 |
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 |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.8%
- 10x: 99.4%
- 20x: 98.5%
|
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2310022B05Rik |
A |
T |
8: 125,366,098 (GRCm39) |
I215N |
probably damaging |
Het |
| Aig1 |
T |
C |
10: 13,528,757 (GRCm39) |
|
probably null |
Het |
| Atp8b2 |
T |
A |
3: 89,861,865 (GRCm39) |
K82N |
possibly damaging |
Het |
| Cacnb4 |
T |
G |
2: 52,359,615 (GRCm39) |
Y131S |
probably damaging |
Het |
| Cep170b |
G |
A |
12: 112,697,864 (GRCm39) |
S62N |
possibly damaging |
Het |
| Crmp1 |
A |
G |
5: 37,422,619 (GRCm39) |
D142G |
probably benign |
Het |
| Csf1r |
A |
G |
18: 61,260,957 (GRCm39) |
Q716R |
possibly damaging |
Het |
| Cyp2u1 |
T |
C |
3: 131,087,133 (GRCm39) |
T483A |
possibly damaging |
Het |
| D930020B18Rik |
T |
C |
10: 121,503,565 (GRCm39) |
F247L |
probably benign |
Het |
| Dcaf13 |
T |
C |
15: 39,008,586 (GRCm39) |
L396P |
probably damaging |
Het |
| Dnhd1 |
A |
G |
7: 105,353,240 (GRCm39) |
M2798V |
probably benign |
Het |
| E030018B13Rik |
A |
T |
7: 63,569,125 (GRCm39) |
T58S |
unknown |
Het |
| Eipr1 |
T |
C |
12: 28,897,657 (GRCm39) |
|
probably null |
Het |
| Elf1 |
C |
T |
14: 79,817,948 (GRCm39) |
T526M |
possibly damaging |
Het |
| Gm8369 |
GTGTGTGTGTGTGTGTGTGTG |
GTGTGTGTGTGTGTGTGTGTGTG |
19: 11,489,128 (GRCm39) |
|
probably null |
Het |
| Got1 |
A |
G |
19: 43,504,284 (GRCm39) |
S46P |
probably benign |
Het |
| Inpp4b |
T |
C |
8: 82,775,160 (GRCm39) |
I786T |
probably benign |
Het |
| Krt222 |
A |
T |
11: 99,125,838 (GRCm39) |
S264R |
probably benign |
Het |
| Lrrd1 |
A |
C |
5: 3,899,982 (GRCm39) |
S96R |
possibly damaging |
Het |
| Ltb |
C |
A |
17: 35,414,906 (GRCm39) |
Y235* |
probably null |
Het |
| Mbd2 |
T |
A |
18: 70,751,050 (GRCm39) |
C362S |
probably damaging |
Het |
| Mlycd |
T |
A |
8: 120,129,325 (GRCm39) |
I264N |
probably damaging |
Het |
| Mri1 |
C |
T |
8: 84,980,933 (GRCm39) |
C199Y |
possibly damaging |
Het |
| Muc5ac |
A |
T |
7: 141,349,021 (GRCm39) |
K487* |
probably null |
Het |
| Myh13 |
T |
C |
11: 67,249,016 (GRCm39) |
I1274T |
probably damaging |
Het |
| Ncdn |
G |
A |
4: 126,642,467 (GRCm39) |
R397W |
probably damaging |
Het |
| Ncf1 |
T |
A |
5: 134,258,444 (GRCm39) |
|
probably benign |
Het |
| Nipbl |
C |
A |
15: 8,321,032 (GRCm39) |
A2692S |
probably benign |
Het |
| Odf2l |
C |
T |
3: 144,854,789 (GRCm39) |
T542I |
possibly damaging |
Het |
| Or10a49 |
A |
G |
7: 108,467,698 (GRCm39) |
I221T |
probably damaging |
Het |
| Or10al2 |
T |
A |
17: 37,983,145 (GRCm39) |
I77N |
probably damaging |
Het |
| Oxsm |
T |
C |
14: 16,242,629 (GRCm38) |
T47A |
possibly damaging |
Het |
| Pcdhga3 |
A |
T |
18: 37,807,786 (GRCm39) |
S80C |
probably benign |
Het |
| Pcnx2 |
T |
C |
8: 126,512,176 (GRCm39) |
T1377A |
probably benign |
Het |
| Phactr3 |
C |
A |
2: 177,924,805 (GRCm39) |
Q252K |
possibly damaging |
Het |
| Phf2 |
T |
C |
13: 48,973,101 (GRCm39) |
H385R |
unknown |
Het |
| Pkd1l3 |
A |
T |
8: 110,357,937 (GRCm39) |
T820S |
probably benign |
Het |
| Plekhg1 |
T |
A |
10: 3,887,966 (GRCm39) |
H353Q |
|
Het |
| Prss37 |
T |
A |
6: 40,494,713 (GRCm39) |
E24V |
probably damaging |
Het |
| Reln |
A |
G |
5: 22,155,943 (GRCm39) |
F2183S |
probably damaging |
Het |
| Slc20a2 |
A |
G |
8: 23,051,407 (GRCm39) |
D480G |
probably damaging |
Het |
| Slc8a2 |
C |
T |
7: 15,887,124 (GRCm39) |
T672M |
probably damaging |
Het |
| Slf2 |
A |
G |
19: 44,961,666 (GRCm39) |
T1062A |
probably benign |
Het |
| Snx29 |
A |
G |
16: 11,223,609 (GRCm39) |
E18G |
possibly damaging |
Het |
| Spata31e1 |
C |
T |
13: 49,939,542 (GRCm39) |
V723M |
possibly damaging |
Het |
| Srf |
C |
A |
17: 46,860,079 (GRCm39) |
G482V |
possibly damaging |
Het |
| Styk1 |
G |
A |
6: 131,287,992 (GRCm39) |
Q124* |
probably null |
Het |
| Tcf7l1 |
G |
T |
6: 72,608,226 (GRCm39) |
A385E |
probably damaging |
Het |
| Thbs4 |
A |
G |
13: 92,913,495 (GRCm39) |
S142P |
probably benign |
Het |
| Tlr1 |
G |
A |
5: 65,083,371 (GRCm39) |
S402F |
probably damaging |
Het |
| Tnrc6a |
A |
G |
7: 122,769,635 (GRCm39) |
H475R |
probably benign |
Het |
| Trmt10b |
A |
T |
4: 45,314,374 (GRCm39) |
N272I |
probably damaging |
Het |
| Ubxn7 |
A |
T |
16: 32,200,471 (GRCm39) |
N409I |
probably benign |
Het |
| Vcan |
T |
C |
13: 89,837,930 (GRCm39) |
E2538G |
probably damaging |
Het |
| Vmn1r65 |
C |
T |
7: 6,011,387 (GRCm39) |
W282* |
probably null |
Het |
| Vmn2r4 |
A |
G |
3: 64,322,497 (GRCm39) |
I74T |
probably benign |
Het |
| Wdr97 |
T |
A |
15: 76,241,125 (GRCm39) |
F574I |
|
Het |
| Zfp949 |
T |
C |
9: 88,449,340 (GRCm39) |
|
probably null |
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 |
|
|
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 |
|
|
X0066:Kdm1a
|
UTSW |
4 |
136,286,536 (GRCm39) |
missense |
probably damaging |
0.98 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCCTGGTCAAGAACTTAAGCTGC -3'
(R):5'- TATTGCTTGCCATTGCCATG -3'
Sequencing Primer
(F):5'- GCCAAAACCCTAGTTCGGTTG -3'
(R):5'- CCATGGAGCCCTTTAAGTGATCAG -3'
|
| Posted On |
2022-11-14 |
Incidental Mutation