Incidental Mutation 'IGL00334:Kdm2a'
ID3272
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm2a
Ensembl Gene ENSMUSG00000054611
Gene Namelysine (K)-specific demethylase 2A
SynonymsGm4560, lalina, Fbl7, Jhdm1a, Cxxc8, Fbxl11, 5530401A10Rik
Accession Numbers
Is this an essential gene? Probably essential (E-score: 0.964) question?
Stock #IGL00334
Quality Score
Status
Chromosome19
Chromosomal Location4314419-4398285 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to T at 4356898 bp
ZygosityHeterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 112 (D112E)
Ref Sequence ENSEMBL: ENSMUSP00000076698 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047898] [ENSMUST00000075856] [ENSMUST00000116571] [ENSMUST00000175959]
Predicted Effect possibly damaging
Transcript: ENSMUST00000047898
AA Change: D112E

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: D112E

DomainStartEndE-ValueType
low complexity region 23 34 N/A INTRINSIC
low complexity region 127 138 N/A INTRINSIC
JmjC 148 316 1.52e-34 SMART
low complexity region 416 433 N/A INTRINSIC
PDB:2YU2|A 440 517 1e-35 PDB
Pfam:zf-CXXC 563 609 7.5e-16 PFAM
PHD 619 676 3.25e-4 SMART
low complexity region 848 875 N/A INTRINSIC
FBOX 892 932 1.58e-2 SMART
low complexity region 987 998 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000075856
AA Change: D112E

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: D112E

DomainStartEndE-ValueType
low complexity region 23 34 N/A INTRINSIC
low complexity region 127 138 N/A INTRINSIC
JmjC 148 316 1.52e-34 SMART
low complexity region 416 433 N/A INTRINSIC
PDB:2YU2|A 440 517 1e-35 PDB
Pfam:zf-CXXC 563 609 7.5e-16 PFAM
PHD 619 676 3.25e-4 SMART
low complexity region 848 875 N/A INTRINSIC
FBOX 892 932 1.58e-2 SMART
low complexity region 987 998 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000116571
AA Change: D112E

PolyPhen 2 Score 0.347 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000139651
Gene: ENSMUSG00000054611
AA Change: D112E

DomainStartEndE-ValueType
low complexity region 23 34 N/A INTRINSIC
low complexity region 127 138 N/A INTRINSIC
JmjC 148 316 5.9e-37 SMART
low complexity region 416 433 N/A INTRINSIC
PDB:2YU2|A 440 493 4e-21 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175682
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175777
Predicted Effect probably benign
Transcript: ENSMUST00000175959
AA Change: D89E

PolyPhen 2 Score 0.127 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000135689
Gene: ENSMUSG00000054611
AA Change: D89E

DomainStartEndE-ValueType
PDB:2YU2|A 1 206 1e-140 PDB
Blast:JmjC 7 79 8e-23 BLAST
Blast:JmjC 125 206 3e-55 BLAST
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 member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains at least six highly degenerated leucine-rich repeats. This family member plays a role in epigenetic silencing. It nucleates at CpG islands and specifically demethylates both mono- and di-methylated lysine-36 of histone H3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
PHENOTYPE: Mice homozygous for a null allele show embryonic lethality, severe growth retardation, reduced neuron proliferation, increased neuron apoptosis, impaired neuron differentiation, small hearts, abnormal cardiac looping and, in some cases, incomplete embryonic turning and neural tube closure defects. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610507B11Rik T A 11: 78,269,574 L620I possibly damaging Het
Arsb T G 13: 93,939,279 H423Q probably benign Het
Ces1f T C 8: 93,267,992 T264A probably benign Het
Clcn6 C A 4: 148,017,902 probably null Het
Cyb5r3 C A 15: 83,160,404 A138S probably benign Het
Cyp3a57 A T 5: 145,371,024 N197Y probably damaging Het
Dctn2 A G 10: 127,277,690 probably benign Het
Dnmt1 C T 9: 20,910,270 A1197T possibly damaging Het
Dock2 T C 11: 34,704,661 D436G probably damaging Het
Drd4 A G 7: 141,292,183 N49S probably damaging Het
Dst T A 1: 34,166,292 V521D probably damaging Het
Eif5b T C 1: 38,041,719 S714P probably damaging Het
Elmsan1 G A 12: 84,172,855 R442* probably null Het
Glis3 A G 19: 28,540,264 I178T probably damaging Het
Gm11565 T A 11: 99,915,195 C138S possibly damaging Het
H1foo T A 6: 115,947,627 probably benign Het
Hdx T A X: 111,582,881 I623F probably benign Het
Huwe1 T G X: 151,885,627 L843V probably damaging Het
Hyal2 T C 9: 107,570,405 Y86H probably damaging Het
Irf7 A T 7: 141,264,640 S157T probably benign Het
Jmjd4 T A 11: 59,455,314 M331K probably damaging Het
Kdelc2 C A 9: 53,398,028 probably benign Het
Kdelc2 T A 9: 53,398,030 probably benign Het
Mamdc2 A C 19: 23,378,774 Y103* probably null Het
Map2k3 T C 11: 60,943,215 V77A possibly damaging Het
Mprip T A 11: 59,748,591 D403E probably benign Het
Mutyh T A 4: 116,819,319 V496D possibly damaging Het
Nbeal1 T C 1: 60,281,883 V2051A probably damaging Het
Nbeal1 T C 1: 60,328,103 L2575P probably damaging Het
Olfr16 T G 1: 172,957,591 S265R possibly damaging Het
Olfr575 T C 7: 102,955,104 K173E probably benign Het
Pcdhb6 T A 18: 37,334,224 I66N probably damaging Het
Pck2 T C 14: 55,542,641 Y89H probably benign Het
Polr3e C T 7: 120,940,811 Q594* probably null Het
Ptpro T G 6: 137,394,909 probably null Het
Rfx4 A G 10: 84,780,053 K28E possibly damaging Het
Shox2 T C 3: 66,981,441 E39G possibly damaging Het
Slc22a16 A T 10: 40,573,934 D122V probably benign Het
Smr3a A C 5: 88,008,060 probably benign Het
Taf4 G T 2: 179,976,625 L8M unknown Het
Tbkbp1 T A 11: 97,137,648 probably benign Het
Tepp G A 8: 95,313,048 R31H probably damaging Het
Tmem120b G T 5: 123,115,167 E210D probably damaging Het
Tmem120b A T 5: 123,115,166 probably null Het
Trim21 C T 7: 102,559,598 V305M probably damaging Het
Ube4a A T 9: 44,948,141 L353Q probably damaging Het
Zfyve1 A T 12: 83,574,798 N274K probably benign Het
Other mutations in Kdm2a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00679:Kdm2a APN 19 4326841 missense probably damaging 1.00
IGL01104:Kdm2a APN 19 4356738 splice site probably benign
IGL01161:Kdm2a APN 19 4319251 missense probably benign 0.04
IGL01433:Kdm2a APN 19 4342860 missense possibly damaging 0.83
IGL01456:Kdm2a APN 19 4351755 missense probably damaging 1.00
IGL01467:Kdm2a APN 19 4324407 missense probably damaging 0.99
IGL01517:Kdm2a APN 19 4362061 splice site probably benign
IGL01528:Kdm2a APN 19 4343055 missense probably benign 0.18
IGL02504:Kdm2a APN 19 4356771 missense possibly damaging 0.92
IGL02895:Kdm2a APN 19 4362902 missense probably damaging 1.00
IGL03109:Kdm2a APN 19 4329107 missense probably benign 0.04
IGL03171:Kdm2a APN 19 4356764 missense probably damaging 1.00
IGL03256:Kdm2a APN 19 4345510 unclassified probably benign
BB009:Kdm2a UTSW 19 4319156 missense probably damaging 0.98
BB019:Kdm2a UTSW 19 4319156 missense probably damaging 0.98
P0027:Kdm2a UTSW 19 4343245 splice site probably benign
PIT4382001:Kdm2a UTSW 19 4343173 missense probably benign
R0220:Kdm2a UTSW 19 4324919 missense possibly damaging 0.85
R0961:Kdm2a UTSW 19 4329191 missense probably benign 0.07
R1662:Kdm2a UTSW 19 4328212 missense probably damaging 1.00
R2023:Kdm2a UTSW 19 4322464 missense probably damaging 0.98
R2191:Kdm2a UTSW 19 4356931 splice site probably null
R2207:Kdm2a UTSW 19 4362870 missense probably damaging 1.00
R2351:Kdm2a UTSW 19 4329126 missense probably benign 0.02
R2406:Kdm2a UTSW 19 4322518 missense probably damaging 1.00
R2882:Kdm2a UTSW 19 4331184 critical splice donor site probably null
R3788:Kdm2a UTSW 19 4351805 missense probably damaging 0.99
R3792:Kdm2a UTSW 19 4324512 missense possibly damaging 0.91
R3950:Kdm2a UTSW 19 4343232 missense possibly damaging 0.89
R4235:Kdm2a UTSW 19 4322521 missense probably damaging 0.98
R4377:Kdm2a UTSW 19 4329054 missense probably benign 0.01
R4466:Kdm2a UTSW 19 4320300 missense probably damaging 0.99
R4766:Kdm2a UTSW 19 4324507 unclassified probably benign
R4824:Kdm2a UTSW 19 4362787 missense probably damaging 1.00
R4838:Kdm2a UTSW 19 4325026 missense probably benign 0.41
R5283:Kdm2a UTSW 19 4331269 missense probably benign 0.00
R6366:Kdm2a UTSW 19 4324932 missense probably benign 0.15
R6368:Kdm2a UTSW 19 4350317 missense probably damaging 1.00
R6522:Kdm2a UTSW 19 4324826 missense possibly damaging 0.49
R6716:Kdm2a UTSW 19 4329102 missense probably damaging 1.00
R6757:Kdm2a UTSW 19 4319243 missense probably damaging 0.98
R6912:Kdm2a UTSW 19 4322501 missense probably benign 0.06
R6996:Kdm2a UTSW 19 4345641 missense probably benign 0.16
R7090:Kdm2a UTSW 19 4319141 missense probably damaging 1.00
R7497:Kdm2a UTSW 19 4324376 missense probably damaging 1.00
R7542:Kdm2a UTSW 19 4333830 start gained probably benign
R7932:Kdm2a UTSW 19 4319156 missense probably damaging 0.98
R8199:Kdm2a UTSW 19 4389026 missense unknown
R8263:Kdm2a UTSW 19 4324364 missense possibly damaging 0.88
R8446:Kdm2a UTSW 19 4356888 nonsense probably null
RF046:Kdm2a UTSW 19 4324507 unclassified probably benign
X0028:Kdm2a UTSW 19 4320271 missense possibly damaging 0.77
X0028:Kdm2a UTSW 19 4348746 missense probably damaging 1.00
Posted On2012-04-20