Incidental Mutation 'R9351:Kdm2a'
ID 708099
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
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R9351 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 4366172-4448749 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 4393141 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Asparagine at position 405 (D405N)
Ref Sequence ENSEMBL: ENSMUSP00000047683 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047898] [ENSMUST00000075856] [ENSMUST00000116571]
AlphaFold no structure available at present
Predicted Effect
SMART Domains Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: D405N

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: D405N

PolyPhen 2 Score 0.383 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: D405N

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: D405N

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000139651
Gene: ENSMUSG00000054611
AA Change: D405N

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
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.8%
Validation Efficiency 100% (54/54)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700113H08Rik A G 10: 87,066,068 (GRCm39) T84A probably benign Het
Abca17 G A 17: 24,510,751 (GRCm39) S909L probably benign Het
Adamtsl3 A T 7: 82,169,929 (GRCm39) Y371F possibly damaging Het
Adcy9 A T 16: 4,236,228 (GRCm39) S394R probably damaging Het
Ahcyl1 T C 3: 107,575,011 (GRCm39) N444S probably damaging Het
Ahnak A C 19: 8,985,232 (GRCm39) D2172A probably damaging Het
Arhgef28 C T 13: 98,130,576 (GRCm39) D421N probably benign Het
Brd1 T A 15: 88,614,307 (GRCm39) E196V possibly damaging Het
Cabs1 A G 5: 88,128,300 (GRCm39) D317G probably damaging Het
Ccdc96 T C 5: 36,642,069 (GRCm39) I25T unknown Het
Clgn A G 8: 84,153,218 (GRCm39) R607G possibly damaging Het
Clp1 T C 2: 84,554,195 (GRCm39) K325E probably benign Het
Dcun1d1 A T 3: 35,975,185 (GRCm39) I52K probably benign Het
Dync2h1 G A 9: 7,176,911 (GRCm39) T16I probably damaging Het
Eif4a3l1 A T 6: 136,306,771 (GRCm39) I411F probably benign Het
Epb41l5 A G 1: 119,477,639 (GRCm39) F711L probably benign Het
Esr1 G A 10: 4,696,763 (GRCm39) W204* probably null Het
Fat2 A G 11: 55,172,127 (GRCm39) L2862P probably damaging Het
Frmd3 A G 4: 74,054,068 (GRCm39) E159G probably damaging Het
Gsto2 T A 19: 47,874,608 (GRCm39) C243S possibly damaging Het
Heg1 A G 16: 33,545,867 (GRCm39) H206R probably benign Het
Ifi203 A G 1: 173,750,133 (GRCm39) V862A probably benign Het
Ippk C T 13: 49,615,107 (GRCm39) H497Y probably benign Het
Irf5 A T 6: 29,531,317 (GRCm39) N61I possibly damaging Het
Iws1 G A 18: 32,213,213 (GRCm39) E214K possibly damaging Het
Kcnj12 C T 11: 60,960,673 (GRCm39) H324Y probably damaging Het
Lars2 A G 9: 123,265,366 (GRCm39) Q474R probably benign Het
Lctl T C 9: 64,040,473 (GRCm39) F472S possibly damaging Het
Map4k2 T C 19: 6,401,223 (GRCm39) S590P probably benign Het
Mcf2l G T 8: 13,050,757 (GRCm39) L337F possibly damaging Het
Mvp A G 7: 126,595,435 (GRCm39) V225A probably damaging Het
Nfat5 T A 8: 108,065,910 (GRCm39) D241E probably damaging Het
Or6n2 T A 1: 173,897,021 (GRCm39) D52E probably benign Het
Pagr1a A T 7: 126,616,073 (GRCm39) H7Q probably damaging Het
Parp8 G T 13: 117,000,781 (GRCm39) Q787K probably damaging Het
Pcdhb2 C A 18: 37,429,369 (GRCm39) N90K probably damaging Het
Pde6h A G 6: 136,936,332 (GRCm39) K25R probably benign Het
Prr35 G A 17: 26,166,118 (GRCm39) Q390* probably null Het
Psd3 C A 8: 68,413,301 (GRCm39) A410S probably benign Het
Pus10 A G 11: 23,617,311 (GRCm39) N8S probably benign Het
Rnf115 T C 3: 96,695,994 (GRCm39) L260S probably damaging Het
Sdsl A T 5: 120,601,159 (GRCm39) Y38N probably benign Het
Sf1 A G 19: 6,415,694 (GRCm39) D11G probably damaging Het
Stxbp5l A G 16: 36,936,047 (GRCm39) Y1177H probably damaging Het
Taar2 G A 10: 23,816,900 (GRCm39) V147I probably benign Het
Tmed3 A T 9: 89,584,980 (GRCm39) F92I possibly damaging Het
Tmprss15 T C 16: 78,832,086 (GRCm39) T357A probably damaging Het
Trbv14 A T 6: 41,112,428 (GRCm39) D75V probably damaging Het
Vmn1r30 A G 6: 58,412,262 (GRCm39) V190A probably benign Het
Vmn2r115 A T 17: 23,578,482 (GRCm39) I652F probably benign Het
Vmn2r26 A T 6: 124,016,333 (GRCm39) M266L probably benign Het
Wdr17 T C 8: 55,143,057 (GRCm39) I198V probably benign Het
Wdr27 G A 17: 15,128,833 (GRCm39) A540V possibly damaging Het
Zfp26 A C 9: 20,349,447 (GRCm39) Y372* probably null Het
Zfp286 A G 11: 62,670,801 (GRCm39) V424A probably damaging 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
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
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'- CGTCTTCTATTCCTGTGGGGAC -3'
(R):5'- GGTCTTGTCATCTATAACTTTGGAC -3'

Sequencing Primer
(F):5'- GCAGTGGCAGTGACTCTAACTTATC -3'
(R):5'- GGACAAAGCTTTTCCTCTTTTTG -3'
Posted On 2022-04-18