Mutagenetix > Incidental Mutation

Incidental Mutation 'R0220:Kdm2a'

33819

Institutional Source

Beutler Lab

Gene Symbol

Kdm2a

Ensembl Gene

ENSMUSG00000054611

Gene Name

lysine (K)-specific demethylase 2A

Synonyms

Gm4560, lalina, Fbl7, Jhdm1a, Cxxc8, Fbxl11, 5530401A10Rik

MMRRC Submission

038469-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R0220 (G1)

Quality Score

189

Status

Not validated

Chromosome

Chromosomal Location

4314419-4398285 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 4324919 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 288 (D288G)

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

possibly damaging
Transcript: ENSMUST00000047898
AA Change: D728G

PolyPhen 2 Score 0.673 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: D728G

Domain	Start	End	E-Value	Type
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: ENSMUST00000075856
AA Change: D728G

PolyPhen 2 Score 0.673 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: D728G

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
low complexity region	24	35	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000176532

Predicted Effect

possibly damaging
Transcript: ENSMUST00000176653
AA Change: D288G

PolyPhen 2 Score 0.848 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000135745
Gene: ENSMUSG00000054611
AA Change: D288G

Domain	Start	End	E-Value	Type
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: 99.2%
3x: 98.6%
10x: 96.9%
20x: 94.6%

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	T	C	12: 71,148,420		probably null	Het
Abcc5	A	G	16: 20,369,102	V863A	probably benign	Het
Anxa6	A	C	11: 54,981,762		probably null	Het
Armc10	A	G	5: 21,661,584	K296R	probably benign	Het
Arpc2	T	A	1: 74,248,134	F38I	probably damaging	Het
Ass1	A	T	2: 31,514,819	N371Y	probably damaging	Het
Bcl6	T	A	16: 23,966,219	H677L	possibly damaging	Het
Bcl7a	G	A	5: 123,351,919	V49I	probably damaging	Het
Ccnj	T	C	19: 40,844,810	L144P	probably damaging	Het
Cdh8	G	T	8: 99,111,679	P510T	probably benign	Het
Cgnl1	C	A	9: 71,724,943	K375N	possibly damaging	Het
Cubn	C	A	2: 13,356,709	R1695L	probably damaging	Het
Cyp3a59	G	A	5: 146,098,270	V253I	probably benign	Het
Cyp4f13	A	G	17: 32,929,502	I208T	probably damaging	Het
Dennd4a	A	C	9: 64,852,445	E277D	probably damaging	Het
Depdc1a	G	A	3: 159,523,905	V625I	probably benign	Het
Dot1l	A	T	10: 80,785,858	D448V	probably damaging	Het
Efhc1	A	G	1: 20,967,358	D253G	probably damaging	Het
Eme1	T	A	11: 94,650,258	E246V	probably null	Het
Foxred1	A	G	9: 35,209,453	L128P	probably damaging	Het
Gm14124	A	T	2: 150,268,675	Q428H	unknown	Het
Gm4787	G	T	12: 81,378,648	S245R	probably damaging	Het
Gm5141	T	A	13: 62,774,457	K299N	probably damaging	Het
Greb1	C	A	12: 16,682,286	R1558L	probably damaging	Het
Ip6k3	A	T	17: 27,145,229	F282I	probably damaging	Het
Kdm4d	A	T	9: 14,463,122	V480E	probably benign	Het
Kif26a	A	T	12: 112,157,390	Q143L	probably damaging	Het
Klhl41	G	A	2: 69,670,485	D97N	probably benign	Het
Krt34	C	T	11: 100,038,693		probably benign	Het
Lcn11	A	T	2: 25,777,831	H77L	probably benign	Het
Megf6	G	A	4: 154,258,215	R529H	probably damaging	Het
Mipol1	A	G	12: 57,457,150	E368G	probably damaging	Het
Mtus1	A	T	8: 40,994,572	M442K	probably damaging	Het
Naca	T	C	10: 128,043,386		probably benign	Het
Nbea	G	A	3: 56,005,303	T1021I	probably benign	Het
Nfib	A	T	4: 82,296,776	V530E	probably damaging	Het
Nptx1	A	G	11: 119,544,641	V283A	probably damaging	Het
Olfr1261	G	T	2: 89,993,862	L156F	probably benign	Het
Olfr190	A	T	16: 59,074,732	M116K	probably damaging	Het
Opn5	A	G	17: 42,596,604	V127A	probably benign	Het
Pcgf6	A	G	19: 47,040,090	V291A	probably benign	Het
Pilrb2	C	A	5: 137,871,197	R47L	probably benign	Het
Prom2	A	C	2: 127,541,107	S72A	probably benign	Het
Sema3e	T	C	5: 14,164,153	F144S	possibly damaging	Het
Sephs1	A	G	2: 4,899,560	T250A	probably benign	Het
Smarcc2	A	T	10: 128,483,636	D798V	probably benign	Het
Taf5	T	C	19: 47,080,560	S563P	probably damaging	Het
Topaz1	A	G	9: 122,749,303	H426R	possibly damaging	Het
Tpgs1	T	A	10: 79,675,437	C138S	possibly damaging	Het
Traf1	A	T	2: 34,949,103	V70D	probably benign	Het
Ttn	T	C	2: 76,811,393	Y13453C	probably damaging	Het
Ubxn4	T	A	1: 128,256,194	V97D	possibly damaging	Het
Ugt1a8	A	T	1: 88,088,335	I157L	probably benign	Het
Vmn2r13	A	T	5: 109,156,466	C700S	probably damaging	Het
Wee1	A	T	7: 110,124,526	D216V	probably benign	Het
Zc3h4	T	C	7: 16,429,273	Y533H	unknown	Het
Zfp81	A	G	17: 33,336,724	I43T	possibly damaging	Het
Zfp963	A	T	8: 69,743,493	Y103*	probably null	Het
Zfp963	A	T	8: 69,743,495	Y103N	probably benign	Het
Zzef1	G	T	11: 72,865,966	D1126Y	probably damaging	Het

Other mutations in Kdm2a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
IGL01433:Kdm2a	APN	19	4342860	missense	possibly damaging	0.83
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
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
R9158:Kdm2a	UTSW	19	4324687	missense	possibly damaging	0.49
R9303:Kdm2a	UTSW	19	4345578	missense	probably benign	0.01
R9314:Kdm2a	UTSW	19	4322482	missense	probably damaging	1.00
R9351:Kdm2a	UTSW	19	4343113	missense
R9353:Kdm2a	UTSW	19	4343113	missense
R9411:Kdm2a	UTSW	19	4362807	missense	probably damaging	0.99
R9456:Kdm2a	UTSW	19	4343113	missense
R9616:Kdm2a	UTSW	19	4320280	missense	probably damaging	0.99
R9625:Kdm2a	UTSW	19	4343113	missense
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

Predicted Primers

PCR Primer
(F):5'- TGGCTTTCTCAACTTCAGACAGCTC -3'
(R):5'- GTAGCAGTGACATGGCTTCTCTCAG -3'

Sequencing Primer
(F):5'- AGACAGCTCCTTTTTGCCG -3'
(R):5'- GACATGGCTTCTCTCAGATTCTAC -3'

Posted On

2013-05-09