Incidental Mutation 'R6366:Kdm2a'
ID 512718
Institutional Source Beutler Lab
Gene Symbol Kdm2a
Ensembl Gene ENSMUSG00000054611
Gene Name lysine (K)-specific demethylase 2A
Synonyms Fbxl11, lalina, Fbl7, 5530401A10Rik, Gm4560, Cxxc8, Jhdm1a
MMRRC Submission 044516-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R6366 (G1)
Quality Score 225.009
Status Not validated
Chromosome 19
Chromosomal Location 4366172-4448749 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 4374960 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Lysine at position 724 (Q724K)
Ref Sequence ENSEMBL: ENSMUSP00000076698 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047898] [ENSMUST00000075856] [ENSMUST00000176497] [ENSMUST00000176653]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000047898
AA Change: Q724K

PolyPhen 2 Score 0.150 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: Q724K

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: Q724K

PolyPhen 2 Score 0.150 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: Q724K

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 noncoding transcript
Transcript: ENSMUST00000175978
Predicted Effect probably benign
Transcript: ENSMUST00000176497
SMART Domains Protein: ENSMUSP00000135471
Gene: ENSMUSG00000054611

DomainStartEndE-ValueType
low complexity region 24 35 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000176532
Predicted Effect probably benign
Transcript: ENSMUST00000176653
AA Change: Q284K

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000135745
Gene: ENSMUSG00000054611
AA Change: Q284K

DomainStartEndE-ValueType
low complexity region 24 35 N/A INTRINSIC
PDB:2YU2|A 52 77 4e-7 PDB
Pfam:zf-CXXC 123 169 3e-16 PFAM
PHD 179 236 3.25e-4 SMART
Meta Mutation Damage Score 0.0738 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.7%
  • 10x: 98.0%
  • 20x: 93.4%
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agl A G 3: 116,584,766 (GRCm39) F185L probably damaging Het
Ank3 A G 10: 69,835,188 (GRCm39) D131G probably damaging Het
Boc T C 16: 44,308,015 (GRCm39) K947E probably benign Het
Ccdc110 A G 8: 46,396,425 (GRCm39) E772G probably damaging Het
Ccdc7a A G 8: 129,582,473 (GRCm39) V1055A unknown Het
Chd1l A G 3: 97,501,476 (GRCm39) V190A probably benign Het
Chl1 C A 6: 103,706,197 (GRCm39) N396K possibly damaging Het
CN725425 T G 15: 91,131,124 (GRCm39) Y420D possibly damaging Het
Col6a1 A T 10: 76,546,804 (GRCm39) I806N unknown Het
Csmd2 A G 4: 128,377,245 (GRCm39) K2042E probably benign Het
Eif4a1 G T 11: 69,561,781 (GRCm39) D15E probably benign Het
Etfb T C 7: 43,102,365 (GRCm39) L119S probably damaging Het
Fbxo42 T A 4: 140,927,260 (GRCm39) S513R probably benign Het
Gys2 C A 6: 142,409,120 (GRCm39) C45F probably benign Het
Hspa1a G A 17: 35,189,500 (GRCm39) P468S probably damaging Het
Lama3 G T 18: 12,615,194 (GRCm39) G1373W probably damaging Het
Lhx1 A T 11: 84,413,034 (GRCm39) F84Y probably damaging Het
Lpxn G A 19: 12,802,163 (GRCm39) V163M probably benign Het
Lrrc7 T C 3: 157,841,012 (GRCm39) Q1389R probably benign Het
Lrtm2 T C 6: 119,294,238 (GRCm39) R298G probably damaging Het
Ltv1 A G 10: 13,056,739 (GRCm39) V268A probably benign Het
Mgat4d T A 8: 84,095,580 (GRCm39) probably null Het
Mknk2 C A 10: 80,507,767 (GRCm39) R33L probably damaging Het
Ms4a1 A G 19: 11,236,062 (GRCm39) S42P probably damaging Het
Muc16 T C 9: 18,557,340 (GRCm39) I2984M unknown Het
Mup12 A C 4: 60,696,657 (GRCm39) F74V probably damaging Het
Nacad A C 11: 6,551,196 (GRCm39) L665R probably benign Het
Pde6a T A 18: 61,398,142 (GRCm39) probably null Het
Plb1 A G 5: 32,471,429 (GRCm39) N579D possibly damaging Het
Podn T A 4: 107,876,001 (GRCm39) I552F possibly damaging Het
Potefam1 A G 2: 110,999,937 (GRCm39) probably null Het
Pramel32 T A 4: 88,547,102 (GRCm39) I106F probably damaging Het
Prl3b1 A T 13: 27,427,875 (GRCm39) M62L probably benign Het
Ptpn13 G T 5: 103,698,919 (GRCm39) R1134L probably damaging Het
Rpl37 T A 15: 5,147,990 (GRCm39) probably null Het
Samd4 T A 14: 47,311,607 (GRCm39) probably null Het
Sh3rf2 T C 18: 42,286,130 (GRCm39) V541A probably benign Het
Shcbp1 A G 8: 4,799,380 (GRCm39) V335A probably damaging Het
Slc7a7 T C 14: 54,612,057 (GRCm39) Y282C probably damaging Het
Spag7 T C 11: 70,555,418 (GRCm39) K125E possibly damaging Het
Spata31e4 T C 13: 50,855,972 (GRCm39) Y537H probably benign Het
Sptan1 T C 2: 29,910,467 (GRCm39) S1831P possibly damaging Het
Stab1 T C 14: 30,863,395 (GRCm39) K2097R probably benign Het
Stk38 A G 17: 29,193,338 (GRCm39) W364R probably benign Het
Tectb G A 19: 55,170,350 (GRCm39) G67D probably damaging Het
Ttll9 G T 2: 152,833,525 (GRCm39) D208Y probably damaging Het
Tyro3 G A 2: 119,647,156 (GRCm39) D758N probably damaging Het
Tyw1 T C 5: 130,310,792 (GRCm39) probably benign Het
Unc5b C T 10: 60,614,091 (GRCm39) A253T probably benign Het
Wtap A T 17: 13,186,945 (GRCm39) probably null Het
Other mutations in Kdm2a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00334:Kdm2a APN 19 4,406,926 (GRCm39) missense possibly damaging 0.94
IGL00679:Kdm2a APN 19 4,376,869 (GRCm39) missense probably damaging 1.00
IGL01104:Kdm2a APN 19 4,406,766 (GRCm39) splice site probably benign
IGL01161:Kdm2a APN 19 4,369,279 (GRCm39) missense probably benign 0.04
IGL01433:Kdm2a APN 19 4,392,888 (GRCm39) missense possibly damaging 0.83
IGL01456:Kdm2a APN 19 4,401,783 (GRCm39) missense probably damaging 1.00
IGL01467:Kdm2a APN 19 4,374,435 (GRCm39) missense probably damaging 0.99
IGL01517:Kdm2a APN 19 4,412,089 (GRCm39) splice site probably benign
IGL01528:Kdm2a APN 19 4,393,083 (GRCm39) missense probably benign 0.18
IGL02504:Kdm2a APN 19 4,406,799 (GRCm39) missense possibly damaging 0.92
IGL02895:Kdm2a APN 19 4,412,930 (GRCm39) missense probably damaging 1.00
IGL03109:Kdm2a APN 19 4,379,135 (GRCm39) missense probably benign 0.04
IGL03171:Kdm2a APN 19 4,406,792 (GRCm39) missense probably damaging 1.00
IGL03256:Kdm2a APN 19 4,395,538 (GRCm39) unclassified probably benign
BB009:Kdm2a UTSW 19 4,369,184 (GRCm39) missense probably damaging 0.98
BB019:Kdm2a UTSW 19 4,369,184 (GRCm39) missense probably damaging 0.98
P0027:Kdm2a UTSW 19 4,393,273 (GRCm39) splice site probably benign
PIT4382001:Kdm2a UTSW 19 4,393,201 (GRCm39) missense probably benign
R0220:Kdm2a UTSW 19 4,374,947 (GRCm39) missense possibly damaging 0.85
R0961:Kdm2a UTSW 19 4,379,219 (GRCm39) missense probably benign 0.07
R1662:Kdm2a UTSW 19 4,378,240 (GRCm39) missense probably damaging 1.00
R2023:Kdm2a UTSW 19 4,372,492 (GRCm39) missense probably damaging 0.98
R2191:Kdm2a UTSW 19 4,406,959 (GRCm39) splice site probably null
R2207:Kdm2a UTSW 19 4,412,898 (GRCm39) missense probably damaging 1.00
R2351:Kdm2a UTSW 19 4,379,154 (GRCm39) missense probably benign 0.02
R2406:Kdm2a UTSW 19 4,372,546 (GRCm39) missense probably damaging 1.00
R2882:Kdm2a UTSW 19 4,381,212 (GRCm39) critical splice donor site probably null
R3788:Kdm2a UTSW 19 4,401,833 (GRCm39) missense probably damaging 0.99
R3792:Kdm2a UTSW 19 4,374,540 (GRCm39) missense possibly damaging 0.91
R3950:Kdm2a UTSW 19 4,393,260 (GRCm39) missense possibly damaging 0.89
R4235:Kdm2a UTSW 19 4,372,549 (GRCm39) missense probably damaging 0.98
R4377:Kdm2a UTSW 19 4,379,082 (GRCm39) missense probably benign 0.01
R4466:Kdm2a UTSW 19 4,370,328 (GRCm39) missense probably damaging 0.99
R4766:Kdm2a UTSW 19 4,374,535 (GRCm39) unclassified probably benign
R4824:Kdm2a UTSW 19 4,412,815 (GRCm39) missense probably damaging 1.00
R4838:Kdm2a UTSW 19 4,375,054 (GRCm39) missense probably benign 0.41
R5283:Kdm2a UTSW 19 4,381,297 (GRCm39) missense probably benign 0.00
R6368:Kdm2a UTSW 19 4,400,345 (GRCm39) missense probably damaging 1.00
R6522:Kdm2a UTSW 19 4,374,854 (GRCm39) missense possibly damaging 0.49
R6716:Kdm2a UTSW 19 4,379,130 (GRCm39) missense probably damaging 1.00
R6757:Kdm2a UTSW 19 4,369,271 (GRCm39) missense probably damaging 0.98
R6912:Kdm2a UTSW 19 4,372,529 (GRCm39) missense probably benign 0.06
R6996:Kdm2a UTSW 19 4,395,669 (GRCm39) missense probably benign 0.16
R7090:Kdm2a UTSW 19 4,369,169 (GRCm39) missense probably damaging 1.00
R7497:Kdm2a UTSW 19 4,374,404 (GRCm39) missense probably damaging 1.00
R7542:Kdm2a UTSW 19 4,383,858 (GRCm39) start gained probably benign
R7932:Kdm2a UTSW 19 4,369,184 (GRCm39) missense probably damaging 0.98
R8199:Kdm2a UTSW 19 4,439,054 (GRCm39) missense unknown
R8263:Kdm2a UTSW 19 4,374,392 (GRCm39) missense possibly damaging 0.88
R8446:Kdm2a UTSW 19 4,406,916 (GRCm39) nonsense probably null
R9158:Kdm2a UTSW 19 4,374,715 (GRCm39) missense possibly damaging 0.49
R9303:Kdm2a UTSW 19 4,395,606 (GRCm39) missense probably benign 0.01
R9314:Kdm2a UTSW 19 4,372,510 (GRCm39) missense probably damaging 1.00
R9351:Kdm2a UTSW 19 4,393,141 (GRCm39) missense
R9353:Kdm2a UTSW 19 4,393,141 (GRCm39) missense
R9411:Kdm2a UTSW 19 4,412,835 (GRCm39) missense probably damaging 0.99
R9456:Kdm2a UTSW 19 4,393,141 (GRCm39) missense
R9616:Kdm2a UTSW 19 4,370,308 (GRCm39) missense probably damaging 0.99
R9625:Kdm2a UTSW 19 4,393,141 (GRCm39) missense
RF046:Kdm2a UTSW 19 4,374,535 (GRCm39) unclassified probably benign
X0028:Kdm2a UTSW 19 4,398,774 (GRCm39) missense probably damaging 1.00
X0028:Kdm2a UTSW 19 4,370,299 (GRCm39) missense possibly damaging 0.77
Predicted Primers PCR Primer
(F):5'- GGCTTTCTCAACTTCAGACAGC -3'
(R):5'- CAGTGACATGGCTTCTCTCAG -3'

Sequencing Primer
(F):5'- AGACAGCTCCTTTTTGCCG -3'
(R):5'- GACATGGCTTCTCTCAGATTCTACG -3'
Posted On 2018-04-27