Incidental Mutation 'IGL01106:Kdm1a'
ID 50904
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 # IGL01106
Quality Score
Status
Chromosome 4
Chromosomal Location 136277851-136330034 bp(-) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) A to G at 136299639 bp (GRCm39)
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 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: 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 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: 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: 29 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atg13 T C 2: 91,526,297 (GRCm39) D12G probably damaging Het
Cmya5 A G 13: 93,221,120 (GRCm39) L3163P probably damaging Het
Cntn2 A G 1: 132,449,622 (GRCm39) probably benign Het
Ddx23 C T 15: 98,548,821 (GRCm39) R327Q probably benign Het
Dlec1 G A 9: 118,931,853 (GRCm39) E91K probably benign Het
Fam13c T C 10: 70,284,646 (GRCm39) probably null Het
Fbn1 T C 2: 125,193,626 (GRCm39) T1398A possibly damaging Het
Frem1 T C 4: 82,840,494 (GRCm39) T1793A probably benign Het
Gprc5b T C 7: 118,583,084 (GRCm39) K262E probably benign Het
Hadh A T 3: 131,034,619 (GRCm39) Y226N possibly damaging Het
Herc1 T A 9: 66,383,720 (GRCm39) probably benign Het
Ikbke A G 1: 131,187,792 (GRCm39) probably benign Het
Iqcg T A 16: 32,855,970 (GRCm39) I202L possibly damaging Het
Kank3 G A 17: 34,036,375 (GRCm39) G81E probably damaging Het
Kcna3 A G 3: 106,945,180 (GRCm39) E481G possibly damaging Het
Klhdc8a A T 1: 132,232,438 (GRCm39) S321C probably benign Het
Kntc1 A G 5: 123,900,666 (GRCm39) K255E probably benign Het
Lhfpl4 T A 6: 113,170,824 (GRCm39) T121S probably benign Het
Lsm11 G A 11: 45,824,490 (GRCm39) Q346* probably null Het
Mcoln3 A G 3: 145,843,019 (GRCm39) T368A probably benign Het
Nlrp4g A T 9: 124,350,452 (GRCm38) noncoding transcript Het
Nol8 A G 13: 49,807,957 (GRCm39) I58V possibly damaging Het
Or5al6 C T 2: 85,976,560 (GRCm39) V173M probably benign Het
Phactr4 A G 4: 132,098,116 (GRCm39) F384S probably benign Het
Prkg1 T A 19: 30,562,678 (GRCm39) I509L probably benign Het
Rims1 T A 1: 22,449,671 (GRCm39) D1019V probably damaging Het
Sclt1 T C 3: 41,629,754 (GRCm39) probably benign Het
Sntg2 T A 12: 30,307,987 (GRCm39) K233* probably null Het
Syt5 T C 7: 4,544,156 (GRCm39) T295A probably damaging Het
Other mutations in Kdm1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00796:Kdm1a APN 4 136,281,558 (GRCm39) missense probably damaging 1.00
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
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 2013-06-21