Incidental Mutation 'IGL01886:Kdm1a'
ID 179157
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
Is this an essential gene? Essential (E-score: 1.000) question?
Stock # IGL01886
Quality Score
Status
Chromosome 4
Chromosomal Location 136550540-136602723 bp(-) (GRCm38)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) A to G at 136561016 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change
Gene Model predicted gene model for transcript(s): [ENSMUST00000105847] [ENSMUST00000116273]
AlphaFold Q6ZQ88
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 null
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 null
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: ENSMUST00000147886
Predicted Effect probably null
Transcript: ENSMUST00000155354
SMART Domains Protein: ENSMUSP00000114268
Gene: ENSMUSG00000036940

DomainStartEndE-ValueType
Pfam:Amino_oxidase 3 250 2.9e-12 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000170979
SMART Domains Protein: ENSMUSP00000131385
Gene: ENSMUSG00000036940

DomainStartEndE-ValueType
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
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: 43 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akt1 C T 12: 112,659,158 V136M probably benign Het
Ankrd34c A T 9: 89,730,265 L8M possibly damaging Het
Anks6 C A 4: 47,044,850 W352L probably damaging Het
Arhgap12 A T 18: 6,027,613 N768K probably damaging Het
C130026I21Rik A G 1: 85,254,186 probably benign Het
Clec7a A T 6: 129,463,177 probably benign Het
Cyp3a13 G A 5: 137,898,820 P411S probably damaging Het
Elavl2 A G 4: 91,264,093 V129A probably damaging Het
Ercc6 T A 14: 32,569,580 S994T possibly damaging Het
Esco1 T A 18: 10,595,262 K8I probably damaging Het
Esr1 T A 10: 4,856,861 I259K probably damaging Het
Filip1l A G 16: 57,571,250 I734V possibly damaging Het
Gm10717 C T 9: 3,025,616 S67L probably benign Het
Gm10718 A T 9: 3,025,118 Y194F probably benign Het
Gm21738 G A 14: 19,416,979 S144L probably benign Het
Grin3a T A 4: 49,702,814 I891F probably damaging Het
Kat7 T C 11: 95,306,133 T27A probably benign Het
Kifc5b T C 17: 26,932,117 V663A probably damaging Het
Lama1 T G 17: 67,807,797 S2314A probably benign Het
Lrrc69 C T 4: 14,703,984 V279I probably benign Het
Mast3 A T 8: 70,782,139 L774Q possibly damaging Het
Med27 C A 2: 29,413,482 P9Q probably damaging Het
Myo5a C A 9: 75,169,090 probably benign Het
Myoz1 T C 14: 20,655,309 K14E probably damaging Het
Neb T C 2: 52,183,845 probably benign Het
Nlrp1a T C 11: 71,123,501 T308A probably benign Het
Olfr364-ps1 A G 2: 37,146,509 Y99C probably damaging Het
Olfr926 G T 9: 38,877,548 C124F probably damaging Het
Orc1 T A 4: 108,603,957 probably null Het
Pnkp G A 7: 44,862,207 A76T probably damaging Het
Polr3h T C 15: 81,917,390 E95G probably damaging Het
Prpf40b T A 15: 99,304,447 M62K unknown Het
Prpf8 C A 11: 75,495,744 Q1075K probably benign Het
Ptprg A G 14: 12,179,280 K766E probably benign Het
Rabgap1l A T 1: 160,342,042 N778K probably damaging Het
Riok3 T A 18: 12,139,385 N204K probably damaging Het
Shank3 A G 15: 89,531,663 K650E probably damaging Het
Sim1 T A 10: 50,984,315 S758T probably damaging Het
Slu7 T G 11: 43,439,260 N171K probably damaging Het
Sult6b2 A G 6: 142,790,126 probably null Het
Taf6l C T 19: 8,778,086 probably null Het
Ubtfl1 G A 9: 18,409,721 V182M possibly damaging Het
Vmn2r-ps159 C T 4: 156,338,254 noncoding transcript 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
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
X0066:Kdm1a UTSW 4 136559225 missense probably damaging 0.98
Posted On 2014-05-07