Incidental Mutation 'IGL01433:Kdm2a'
ID84236
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: 0.967) question?
Stock #IGL01433
Quality Score
Status
Chromosome19
Chromosomal Location4314419-4398285 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to G at 4342860 bp
ZygosityHeterozygous
Amino Acid Change Isoleucine to Threonine at position 489 (I489T)
Ref Sequence ENSEMBL: ENSMUSP00000139651 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047898] [ENSMUST00000075856] [ENSMUST00000116571]
Predicted Effect probably benign
Transcript: ENSMUST00000047898
AA Change: I489T

PolyPhen 2 Score 0.225 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: I489T

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
AA Change: I489T

PolyPhen 2 Score 0.225 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: I489T

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: ENSMUST00000116571
AA Change: I489T

PolyPhen 2 Score 0.834 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000139651
Gene: ENSMUSG00000054611
AA Change: I489T

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
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700011H14Rik G T 14: 49,235,884 T128K probably benign Het
4932438A13Rik T G 3: 36,887,770 S241R probably damaging Het
9030624J02Rik A G 7: 118,774,051 probably null Het
Actrt3 C T 3: 30,598,039 G302D probably damaging Het
Adam19 T C 11: 46,112,783 L146P probably damaging Het
Adcy8 T A 15: 64,737,414 Y852F possibly damaging Het
Arfgef1 T C 1: 10,153,432 T1520A probably damaging Het
Atp8b1 C T 18: 64,573,519 V199I probably benign Het
Avl9 A G 6: 56,753,397 D575G probably damaging Het
Bcam C A 7: 19,760,182 V395L possibly damaging Het
Cgn T A 3: 94,779,459 N178Y probably damaging Het
D5Ertd579e A T 5: 36,618,754 D168E probably damaging Het
Dnah17 G T 11: 118,049,934 T3288K probably damaging Het
Ednrb A T 14: 103,843,190 I96N probably damaging Het
Gdpd3 A G 7: 126,771,184 I264V possibly damaging Het
Itih4 T C 14: 30,895,448 V575A probably benign Het
Jhy G A 9: 40,917,216 R465C possibly damaging Het
Kcna4 C T 2: 107,296,733 S604F probably damaging Het
Kcnj6 A G 16: 94,832,955 V99A probably benign Het
Kif13a A G 13: 46,772,908 S241P probably damaging Het
Lax1 T C 1: 133,680,399 I201M probably benign Het
Lzic T A 4: 149,488,147 S65T probably benign Het
March9 T C 10: 127,056,693 T309A probably benign Het
Ndufc1 T C 3: 51,407,376 K70E possibly damaging Het
Olfr635 A T 7: 103,979,332 I53F probably damaging Het
Optn T C 2: 5,027,144 K504R probably benign Het
Pagr1a A G 7: 127,015,475 probably benign Het
Pold1 G A 7: 44,543,232 probably benign Het
Ptprq A G 10: 107,576,880 I1786T probably damaging Het
Rgs20 T C 1: 5,070,077 D34G possibly damaging Het
Rnps1 T C 17: 24,424,545 probably null Het
Rpgrip1 T C 14: 52,126,377 V261A probably damaging Het
Sfxn1 A G 13: 54,093,916 N220S probably benign Het
Slc35f1 T A 10: 53,073,446 probably benign Het
Slc5a4b T C 10: 76,070,495 probably benign Het
Snx19 A G 9: 30,428,771 I402V possibly damaging Het
Spaca6 T C 17: 17,831,167 V35A probably benign Het
Taar2 A G 10: 23,940,759 T66A probably benign Het
Tanc2 C T 11: 105,810,522 H288Y possibly damaging Het
Tbc1d31 A G 15: 57,940,768 Q393R probably benign Het
Trpm1 A G 7: 64,204,528 Y133C probably damaging Het
Vmn2r105 T C 17: 20,228,555 D120G probably benign Het
Vmn2r56 C A 7: 12,715,614 M232I probably benign Het
Zfp251 C T 15: 76,854,555 V113I probably benign 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
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 On2013-11-11