Incidental Mutation 'R5800:Kdm1a'
ID 447339
Institutional Source Beutler Lab
Gene Symbol Kdm1a
Ensembl Gene ENSMUSG00000036940
Gene Name lysine (K)-specific demethylase 1A
Synonyms 1810043O07Rik, Kdm1, LSD1, Aof2
MMRRC Submission 043389-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5800 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 136277851-136330034 bp(-) (GRCm39)
Type of Mutation splice site (3 bp from exon)
DNA Base Change (assembly) T to A at 136300381 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Gene Model predicted gene model for transcript(s): [ENSMUST00000105847] [ENSMUST00000116273]
AlphaFold Q6ZQ88
Predicted Effect probably null
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 probably benign
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
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency 96% (50/52)
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 A T 1: 71,360,591 (GRCm39) V540D possibly damaging Het
Adamts8 A T 9: 30,865,778 (GRCm39) D442V probably damaging Het
B3galt9 T C 2: 34,728,654 (GRCm39) F151S possibly damaging Het
Bltp1 A G 3: 37,106,592 (GRCm39) D4974G probably damaging Het
Casp4 G A 9: 5,308,915 (GRCm39) probably null Het
Cfap45 T A 1: 172,366,167 (GRCm39) V30E probably damaging Het
Col6a4 A G 9: 105,957,474 (GRCm39) F117L probably damaging Het
Dnah7c A T 1: 46,686,175 (GRCm39) T1810S probably benign Het
Drosha C T 15: 12,865,153 (GRCm39) T627M probably damaging Het
Drosha C A 15: 12,902,733 (GRCm39) A1001D probably damaging Het
Efhc1 G A 1: 21,049,005 (GRCm39) V473I probably benign Het
Ephx2 T C 14: 66,344,751 (GRCm39) K191R probably benign Het
Ero1b T A 13: 12,617,190 (GRCm39) probably null Het
Esyt2 A T 12: 116,333,808 (GRCm39) D837V possibly damaging Het
Fip1l1 T A 5: 74,706,742 (GRCm39) D126E possibly damaging Het
Fyttd1 C T 16: 32,711,658 (GRCm39) R86C probably damaging Het
Gm12888 T A 4: 121,176,625 (GRCm39) T59S probably damaging Het
Gm7353 A T 7: 3,160,168 (GRCm39) noncoding transcript Het
Gpr153 C T 4: 152,364,534 (GRCm39) Q197* probably null Het
Grep1 G A 17: 23,936,966 (GRCm39) P72S probably damaging Het
H2-T23 G T 17: 36,342,496 (GRCm39) probably benign Het
Ighv1-16 T A 12: 114,629,531 (GRCm39) R85S probably benign Het
Ipcef1 T A 10: 6,840,569 (GRCm39) D376V probably damaging Het
Klk1b27 A T 7: 43,705,088 (GRCm39) Q85L probably benign Het
Krt39 A T 11: 99,411,971 (GRCm39) D38E probably benign Het
L1td1 T C 4: 98,621,999 (GRCm39) L187P possibly damaging Het
Lrrc8b C T 5: 105,629,208 (GRCm39) S518L probably benign Het
Lyg1 C T 1: 37,986,034 (GRCm39) D176N probably damaging Het
Mctp1 A G 13: 76,836,678 (GRCm39) N82D probably damaging Het
Muc6 T C 7: 141,226,690 (GRCm39) probably benign Het
Nynrin T C 14: 56,108,088 (GRCm39) L1065P probably damaging Het
Or5b118 T C 19: 13,449,260 (GRCm39) S309P probably benign Het
Pcdh7 T A 5: 57,879,567 (GRCm39) S1041T probably damaging Het
Pkd1l1 T A 11: 8,811,302 (GRCm39) M1518L probably benign Het
Prl8a6 G T 13: 27,619,453 (GRCm39) Q90K probably benign Het
Ptcd1 T A 5: 145,096,475 (GRCm39) D206V probably damaging Het
Rap1gap C A 4: 137,447,688 (GRCm39) D478E probably benign Het
Scn5a A G 9: 119,330,732 (GRCm39) Y1269H probably damaging Het
Sdc2 A T 15: 33,028,290 (GRCm39) H136L probably benign Het
Senp6 A T 9: 80,033,715 (GRCm39) I120F probably damaging Het
Shisa5 G A 9: 108,885,162 (GRCm39) probably null Het
Slc19a1 A G 10: 76,878,103 (GRCm39) S213G probably null Het
Smim8 TTTAATGAAGAGCT TT 4: 34,771,261 (GRCm39) probably benign Het
Tbc1d20 T A 2: 152,150,245 (GRCm39) probably null Het
Tll2 T C 19: 41,093,373 (GRCm39) H481R probably benign Het
Tmc7 A G 7: 118,138,663 (GRCm39) V692A probably benign Het
Tmem234 T C 4: 129,500,924 (GRCm39) probably null Het
Vmn1r237 C G 17: 21,535,069 (GRCm39) T264S probably benign Het
Vmn2r98 A T 17: 19,286,260 (GRCm39) T253S probably benign Het
Zfyve27 T C 19: 42,171,102 (GRCm39) Y191H probably damaging 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
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
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
Predicted Primers PCR Primer
(F):5'- TCTTCCTAAAACCTTCTCAAACAGG -3'
(R):5'- TGTGTGTATGAAGGCTTCACAC -3'

Sequencing Primer
(F):5'- CCTTCTCAAACAGGAAATTCGAAG -3'
(R):5'- TGTGTATGAAGGCTTCACACTAGAG -3'
Posted On 2016-12-15