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) question?
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

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 unknown
Transcript: ENSMUST00000046846
AA Change: R498H
SMART Domains Protein: ENSMUSP00000035457
Gene: ENSMUSG00000036940
AA Change: R498H

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 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

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 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

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: 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

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: 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
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
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
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
AlleleSourceChrCoordTypePredicted EffectPPH 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