Incidental Mutation 'IGL01517:Kdm2a'
ID90450
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 #IGL01517
Quality Score
Status
Chromosome19
Chromosomal Location4314419-4398285 bp(-) (GRCm38)
Type of Mutationsplice site
DNA Base Change (assembly) A to G at 4362061 bp
ZygosityHeterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000135689 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047898] [ENSMUST00000075856] [ENSMUST00000116571] [ENSMUST00000175959]
Predicted Effect probably benign
Transcript: ENSMUST00000047898
SMART Domains Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611

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: ENSMUST00000075856
SMART Domains Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611

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
SMART Domains Protein: ENSMUSP00000139651
Gene: ENSMUSG00000054611

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
SMART Domains Protein: ENSMUSP00000135689
Gene: ENSMUSG00000054611

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: 34 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts6 A T 13: 104,390,192 probably benign Het
Arpc1b A G 5: 145,127,869 probably benign Het
Ccdc54 G A 16: 50,589,917 L329F possibly damaging Het
Cdc42bpg G A 19: 6,318,437 R1055H probably damaging Het
Cylc1 A G X: 111,119,030 T29A possibly damaging Het
Ddx50 T C 10: 62,647,132 T53A probably benign Het
Dmap1 G A 4: 117,676,009 R283C probably damaging Het
Extl3 A T 14: 65,076,707 L342H probably damaging Het
Gjb3 A C 4: 127,326,121 I206S probably damaging Het
Gphn T A 12: 78,376,374 I53K probably damaging Het
Gpr22 C T 12: 31,708,710 probably benign Het
Inpp5b T A 4: 124,782,436 C362S probably benign Het
Iqgap3 C A 3: 88,109,396 Q1062K probably benign Het
Ltbp3 A G 19: 5,757,732 D1167G possibly damaging Het
Mpo A G 11: 87,795,821 N65D possibly damaging Het
Mrpl2 A G 17: 46,649,983 R268G probably damaging Het
Nfkbia C T 12: 55,490,645 A220T probably damaging Het
Nlrc3 T A 16: 3,947,487 I1091F probably damaging Het
Notch2 T A 3: 98,138,655 S1674R probably benign Het
Olfr298 T C 7: 86,489,557 probably benign Het
Olfr63 T A 17: 33,269,655 N310K probably benign Het
Pde8b A G 13: 95,100,887 probably null Het
Pla2r1 A G 2: 60,504,253 Y392H probably damaging Het
Plekhm1 A T 11: 103,394,783 N275K possibly damaging Het
Prdm16 T C 4: 154,328,425 H1041R probably damaging Het
Rapsn C A 2: 91,036,618 N88K probably damaging Het
Rasef T A 4: 73,769,822 Q31H probably benign Het
Rpl28-ps4 T C 6: 117,213,852 noncoding transcript Het
Trpc7 T C 13: 56,861,065 Y263C probably damaging Het
Ttn T C 2: 76,747,596 T24318A probably damaging Het
Vmn1r35 T C 6: 66,679,450 T79A probably benign Het
Vmn2r100 T A 17: 19,521,963 S200T probably benign Het
Wnt9b A G 11: 103,731,081 V250A probably benign Het
Zyg11a T A 4: 108,201,194 K383M probably null Het
Other mutations in Kdm2a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00334:Kdm2a APN 19 4356898 missense possibly damaging 0.94
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
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 On2013-12-09