Incidental Mutation 'R6716:Kdm2a'
ID 529409
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 044834-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R6716 (G1)
Quality Score 225.009
Status Not validated
Chromosome 19
Chromosomal Location 4366172-4448749 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 4379130 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 122 (S122P)
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 damaging
Transcript: ENSMUST00000047898
AA Change: S562P

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: S562P

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 damaging
Transcript: ENSMUST00000075856
AA Change: S562P

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: S562P

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: ENSMUST00000176497
SMART Domains Protein: ENSMUSP00000135471
Gene: ENSMUSG00000054611

DomainStartEndE-ValueType
low complexity region 24 35 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000176653
AA Change: S122P

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000135745
Gene: ENSMUSG00000054611
AA Change: S122P

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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.3%
  • 20x: 95.4%
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: 19 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Bmp7 C T 2: 172,714,682 (GRCm39) A376T probably damaging Het
Bnip2 T C 9: 69,910,943 (GRCm39) I296T probably damaging Het
Chrm2 T A 6: 36,501,370 (GRCm39) I409N probably damaging Het
Fat3 T A 9: 15,830,565 (GRCm39) T4310S probably benign Het
Krt20 T C 11: 99,322,754 (GRCm39) T294A possibly damaging Het
Macf1 C T 4: 123,402,231 (GRCm39) S635N probably damaging Het
Nphs2 A G 1: 156,148,637 (GRCm39) S242G probably benign Het
Prss23 A C 7: 89,159,055 (GRCm39) I338S probably damaging Het
Rab11fip3 G T 17: 26,210,031 (GRCm39) S1028R probably damaging Het
Rlig1 T G 10: 100,409,478 (GRCm39) I312L probably benign Het
Sec23a C T 12: 59,015,609 (GRCm39) G711D probably benign Het
Slc50a1 T C 3: 89,177,214 (GRCm39) T68A probably damaging Het
Sphkap C T 1: 83,339,949 (GRCm39) probably null Het
Tas2r122 A T 6: 132,688,860 (GRCm39) I11N probably damaging Het
Tpr C T 1: 150,290,516 (GRCm39) R782C probably damaging Het
Vps13c T C 9: 67,858,749 (GRCm39) L2733P probably benign Het
Vtn C T 11: 78,391,052 (GRCm39) R211C probably damaging Het
Xrcc1 T C 7: 24,266,571 (GRCm39) probably null Het
Zc2hc1b T C 10: 13,047,027 (GRCm39) D28G 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
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'- GCCTTGCAAAATTTTCACTCGG -3'
(R):5'- ACATCTCTTTGCCAGTCCTAGG -3'

Sequencing Primer
(F):5'- GGATCACTTACTGCTAAGCACTG -3'
(R):5'- GTCCTAGGCCAGGTACATTACAG -3'
Posted On 2018-08-01