Incidental Mutation 'R4766:Kdm2a'
ID 366192
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 042407-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R4766 (G1)
Quality Score 107
Status Validated
Chromosome 19
Chromosomal Location 4366172-4448749 bp(-) (GRCm39)
Type of Mutation unclassified
DNA Base Change (assembly) TTCCTCCTCCTCCTCCTCTTCCTCCTCCTC to TTCCTCCTCCTCCTCTTCCTCCTCCTC at 4374535 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000135745 (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
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 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
SMART Domains Protein: ENSMUSP00000135745
Gene: ENSMUSG00000054611

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 0.0846 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency 97% (87/90)
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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2900026A02Rik C T 5: 113,245,502 (GRCm39) V1584I probably benign Het
Adamts12 A G 15: 11,285,987 (GRCm39) D732G probably benign Het
Agpat4 A G 17: 12,370,637 (GRCm39) probably benign Het
AI182371 T C 2: 34,985,829 (GRCm39) D140G possibly damaging Het
Apol11b T A 15: 77,519,133 (GRCm39) T316S probably benign Het
Arsi G A 18: 61,049,723 (GRCm39) G202E probably benign Het
Bard1 T C 1: 71,114,333 (GRCm39) E216G probably benign Het
Bdp1 C A 13: 100,186,376 (GRCm39) R1692L probably damaging Het
Capn10 T C 1: 92,871,141 (GRCm39) I101T probably damaging Het
Ccdc175 C T 12: 72,158,979 (GRCm39) M653I probably benign Het
Ccdc9b C A 2: 118,590,058 (GRCm39) R262L probably damaging Het
Ccr8 G A 9: 119,923,530 (GRCm39) C215Y probably damaging Het
Cct3 T A 3: 88,219,092 (GRCm39) L241* probably null Het
Cd2ap A T 17: 43,163,350 (GRCm39) I25N probably damaging Het
Cdh19 T C 1: 110,820,990 (GRCm39) K583E probably benign Het
Cela3a A G 4: 137,129,986 (GRCm39) S212P unknown Het
Cfap44 T A 16: 44,236,246 (GRCm39) probably null Het
Clca3a1 A T 3: 144,455,473 (GRCm39) L440Q probably damaging Het
Crybg2 A G 4: 133,816,663 (GRCm39) Y1676C probably damaging Het
Dscam T C 16: 96,445,188 (GRCm39) D1501G probably benign Het
Eml6 C A 11: 29,755,757 (GRCm39) L832F probably benign Het
Enpp3 A G 10: 24,649,825 (GRCm39) L867P probably damaging Het
Erbb3 A G 10: 128,422,107 (GRCm39) Y46H possibly damaging Het
Fads3 T C 19: 10,033,384 (GRCm39) I342T possibly damaging Het
Flvcr1 A T 1: 190,753,303 (GRCm39) S290T probably benign Het
Fut9 A G 4: 25,799,191 (GRCm39) probably benign Het
Gad2 C T 2: 22,512,679 (GRCm39) A2V probably damaging Het
Gkn3 C T 6: 87,360,507 (GRCm39) A163T probably damaging Het
Gm10715 T G 9: 3,038,073 (GRCm39) probably benign Het
Herc1 T G 9: 66,349,211 (GRCm39) D2023E probably benign Het
Hsd3b3 A G 3: 98,649,801 (GRCm39) L174P probably damaging Het
Impg2 TACCACCACCACCACCACCACCACCA TACCACCACCACCACCACCACCA 16: 56,078,302 (GRCm39) probably benign Het
Iqcf3 A G 9: 106,438,148 (GRCm39) probably null Het
Kcna4 G A 2: 107,126,888 (GRCm39) V541M probably damaging Het
Kcnj11 T C 7: 45,749,240 (GRCm39) T28A probably benign Het
Kcnmb2 T A 3: 32,236,016 (GRCm39) N88K probably damaging Het
Krt1c T C 15: 101,722,395 (GRCm39) E430G probably damaging Het
Lins1 C T 7: 66,360,389 (GRCm39) L384F possibly damaging Het
Man1c1 G C 4: 134,430,749 (GRCm39) P11R probably damaging Het
Mfge8 T C 7: 78,784,273 (GRCm39) N389D probably damaging Het
Mug1 C T 6: 121,861,213 (GRCm39) T1278I probably benign Het
Myh9 T C 15: 77,692,077 (GRCm39) M161V probably damaging Het
Myl7 T A 11: 5,848,171 (GRCm39) Y61F probably benign Het
Nlrp4d A T 7: 10,096,706 (GRCm39) unknown Het
Nol3 A G 8: 106,008,565 (GRCm39) probably null Het
Nup85 T A 11: 115,468,751 (GRCm39) probably null Het
Obscn T A 11: 58,903,568 (GRCm39) T7619S probably damaging Het
Or2t49 T A 11: 58,392,494 (GRCm39) N296I probably damaging Het
Or4k48 T C 2: 111,476,226 (GRCm39) M39V probably benign Het
Or52a24 C T 7: 103,381,457 (GRCm39) T108I possibly damaging Het
Or7g26 G A 9: 19,230,141 (GRCm39) V104I probably benign Het
Pax5 T A 4: 44,679,494 (GRCm39) I184F probably damaging Het
Pcdha7 T A 18: 37,107,560 (GRCm39) V195D probably damaging Het
Phf3 A T 1: 30,853,020 (GRCm39) probably benign Het
Pla2g15 G T 8: 106,889,703 (GRCm39) G325V probably damaging Het
Ppp1r21 T C 17: 88,880,043 (GRCm39) F487L probably benign Het
Ppp1r9a A G 6: 5,157,016 (GRCm39) I965V probably benign Het
Ptpru A G 4: 131,548,275 (GRCm39) V74A probably damaging Het
Rif1 T A 2: 51,988,946 (GRCm39) Y780N probably damaging Het
Rps25 T A 9: 44,320,046 (GRCm39) Y23N possibly damaging Het
Ryr1 T C 7: 28,785,258 (GRCm39) D1811G probably damaging Het
Scamp5 T G 9: 57,359,319 (GRCm39) probably null Het
Senp1 T C 15: 97,943,777 (GRCm39) D602G probably damaging Het
Sh2b2 T G 5: 136,260,811 (GRCm39) D135A probably damaging Het
Slc26a8 G A 17: 28,857,635 (GRCm39) T836M probably benign Het
Slfn4 T G 11: 83,077,647 (GRCm39) I145S possibly damaging Het
Spag6l G A 16: 16,595,254 (GRCm39) T377I probably benign Het
Spdye4b T C 5: 143,182,089 (GRCm39) F129S probably damaging Het
Sspo G A 6: 48,447,514 (GRCm39) G2360E probably benign Het
Taar2 A T 10: 23,816,669 (GRCm39) I70F probably damaging Het
Taar7e A G 10: 23,914,464 (GRCm39) N318S probably damaging Het
Tor1a C A 2: 30,857,742 (GRCm39) R42L probably benign Het
Trdn A T 10: 33,350,502 (GRCm39) Q690H probably benign Het
Trim56 C A 5: 137,141,579 (GRCm39) V646L probably benign Het
Tspan15 T A 10: 62,027,323 (GRCm39) K165I probably benign Het
Usp24 A G 4: 106,273,245 (GRCm39) Y2210C probably damaging Het
Usp45 A G 4: 21,797,307 (GRCm39) T76A probably damaging Het
Vps13c T A 9: 67,785,506 (GRCm39) probably null Het
Zfp512b T C 2: 181,226,888 (GRCm39) probably benign Het
Zyx C A 6: 42,333,093 (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
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
R6366:Kdm2a UTSW 19 4,374,960 (GRCm39) missense probably benign 0.15
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'- AATATCAAGGTGCACATAGAAGCCC -3'
(R):5'- AAAGAGCTCCACGGGACATC -3'

Sequencing Primer
(F):5'- GTGCACATAGAAGCCCTGTCAC -3'
(R):5'- GACATCCATTGTGCCCAAGCTG -3'
Posted On 2015-12-21