Incidental Mutation 'IGL02605:Kdm1a'
ID300251
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm1a
Ensembl Gene ENSMUSG00000036940
Gene Namelysine (K)-specific demethylase 1A
SynonymsAof2, 1810043O07Rik, Kdm1, LSD1
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL02605
Quality Score
Status
Chromosome4
Chromosomal Location136550540-136602723 bp(-) (GRCm38)
Type of Mutationunclassified
DNA Base Change (assembly) G to T at 136551037 bp
ZygosityHeterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000130758 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001116] [ENSMUST00000063021] [ENSMUST00000105847] [ENSMUST00000105849] [ENSMUST00000116273] [ENSMUST00000168936] [ENSMUST00000170102]
Predicted Effect probably benign
Transcript: ENSMUST00000001116
SMART Domains Protein: ENSMUSP00000001116
Gene: ENSMUSG00000001089

DomainStartEndE-ValueType
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: ENSMUST00000046846
SMART Domains Protein: ENSMUSP00000035457
Gene: ENSMUSG00000036940

DomainStartEndE-ValueType
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: ENSMUST00000063021
SMART Domains Protein: ENSMUSP00000060619
Gene: ENSMUSG00000001089

DomainStartEndE-ValueType
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: ENSMUST00000105847
SMART Domains Protein: ENSMUSP00000101473
Gene: ENSMUSG00000036940

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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
SMART Domains Protein: ENSMUSP00000111977
Gene: ENSMUSG00000036940

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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 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: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abtb2 A T 2: 103,717,257 Y992F probably benign Het
Adgrg6 T A 10: 14,467,232 N324Y probably damaging Het
Ampd3 T C 7: 110,795,758 F305L probably benign Het
Ankrd35 A G 3: 96,681,072 probably null Het
Api5 A G 2: 94,429,719 I64T possibly damaging Het
Arhgap21 A G 2: 20,855,588 I1165T probably damaging Het
Bdp1 T C 13: 100,078,115 probably null Het
Capn3 T A 2: 120,496,037 I570N probably damaging Het
Catsperg2 T C 7: 29,719,565 H232R possibly damaging Het
Clcn7 T C 17: 25,146,818 L156P possibly damaging Het
Cpa3 C A 3: 20,222,212 V286F probably benign Het
Csrnp3 G A 2: 66,022,809 C527Y probably damaging Het
Dock5 A T 14: 67,828,438 V372E probably benign Het
Elmo1 T C 13: 20,605,202 L696P probably damaging Het
Fam91a1 T C 15: 58,431,196 probably benign Het
Gm12695 T A 4: 96,762,751 D155V probably null Het
Hspa4l A G 3: 40,781,623 I559V probably benign Het
Lrrc8d A T 5: 105,826,817 noncoding transcript Het
Minpp1 A T 19: 32,498,415 Y316F possibly damaging Het
Neto2 T C 8: 85,663,435 probably benign Het
Nrxn2 T A 19: 6,450,580 D277E probably benign Het
Ola1 A G 2: 73,142,300 probably benign Het
Olfr1298 A G 2: 111,645,505 V164A probably benign Het
Olfr550 T C 7: 102,579,395 I300T probably damaging Het
Olfr893 T A 9: 38,209,236 M61K probably damaging Het
Pam A G 1: 97,840,339 V722A possibly damaging Het
Pfdn6 T C 17: 33,939,103 Y90C probably benign Het
Pkhd1 T A 1: 20,550,902 H844L possibly damaging Het
Plk5 G A 10: 80,363,062 V422M probably damaging Het
Psmc1 G T 12: 100,119,127 R249L probably damaging Het
Ptpro C T 6: 137,380,318 P269L probably benign Het
Ralgapa1 G T 12: 55,712,665 H1480Q possibly damaging Het
Rars G A 11: 35,824,526 probably benign Het
Rbm48 G A 5: 3,590,600 R260C possibly damaging Het
Smarcc1 C T 9: 110,222,000 H963Y possibly damaging Het
Spef2 T C 15: 9,725,152 E230G probably damaging Het
Spg11 A G 2: 122,092,260 S903P probably benign Het
Tas2r122 T C 6: 132,711,609 Y107C probably damaging Het
Tpm3 C A 3: 90,088,446 N204K probably benign Het
Wdr36 T C 18: 32,851,991 I450T possibly damaging Het
Other mutations in Kdm1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00796:Kdm1a APN 4 136554247 missense probably damaging 1.00
IGL01106:Kdm1a APN 4 136572328 splice site probably benign
IGL01356:Kdm1a APN 4 136553891 missense probably damaging 1.00
IGL01886:Kdm1a APN 4 136561016 critical splice donor site probably null
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 intron 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
X0066:Kdm1a UTSW 4 136559225 missense probably damaging 0.98
Posted On2015-04-16