Mutagenetix > Incidental Mutation

Incidental Mutation 'R4766:Kdm2a'

366192

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

042407-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R4766 (G1)

Quality Score

107

Status

Validated

Chromosome

Chromosomal Location

4314419-4398285 bp(-) (GRCm38)

Type of Mutation

unclassified

DNA Base Change (assembly)

TTCCTCCTCCTCCTCCTCTTCCTCCTCCTC to TTCCTCCTCCTCCTCTTCCTCCTCCTC at 4324507 bp (GRCm38)

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

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

probably benign
Transcript: ENSMUST00000075856

SMART Domains

Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611

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

probably benign
Transcript: ENSMUST00000176653

SMART Domains

Protein: ENSMUSP00000135745
Gene: ENSMUSG00000054611

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

Meta Mutation Damage Score

0.0846

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
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900026A02Rik	C	T	5: 113,097,636	V1584I	probably benign	Het
A430105I19Rik	C	A	2: 118,759,577	R262L	probably damaging	Het
Adamts12	A	G	15: 11,285,901	D732G	probably benign	Het
Agpat4	A	G	17: 12,151,750		probably benign	Het
AI182371	T	C	2: 35,095,817	D140G	possibly damaging	Het
Apol11b	T	A	15: 77,634,933	T316S	probably benign	Het
Arsi	G	A	18: 60,916,651	G202E	probably benign	Het
Bard1	T	C	1: 71,075,174	E216G	probably benign	Het
Bdp1	C	A	13: 100,049,868	R1692L	probably damaging	Het
Capn10	T	C	1: 92,943,419	I101T	probably damaging	Het
Ccdc175	C	T	12: 72,112,205	M653I	probably benign	Het
Ccr8	G	A	9: 120,094,464	C215Y	probably damaging	Het
Cct3	T	A	3: 88,311,785	L241*	probably null	Het
Cd2ap	A	T	17: 42,852,459	I25N	probably damaging	Het
Cdh19	T	C	1: 110,893,260	K583E	probably benign	Het
Cela3a	A	G	4: 137,402,675	S212P	unknown	Het
Cfap44	T	A	16: 44,415,883		probably null	Het
Clca3a1	A	T	3: 144,749,712	L440Q	probably damaging	Het
Crybg2	A	G	4: 134,089,352	Y1676C	probably damaging	Het
Dscam	T	C	16: 96,643,988	D1501G	probably benign	Het
Eml6	C	A	11: 29,805,757	L832F	probably benign	Het
Enpp3	A	G	10: 24,773,927	L867P	probably damaging	Het
Erbb3	A	G	10: 128,586,238	Y46H	possibly damaging	Het
Fads3	T	C	19: 10,056,020	I342T	possibly damaging	Het
Flvcr1	A	T	1: 191,021,106	S290T	probably benign	Het
Fut9	A	G	4: 25,799,191		probably benign	Het
Gad2	C	T	2: 22,622,667	A2V	probably damaging	Het
Gkn3	C	T	6: 87,383,525	A163T	probably damaging	Het
Gm10715	T	G	9: 3,038,073		probably benign	Het
Herc1	T	G	9: 66,441,929	D2023E	probably benign	Het
Hsd3b3	A	G	3: 98,742,485	L174P	probably damaging	Het
Impg2	TACCACCACCACCACCACCACCACCA	TACCACCACCACCACCACCACCA	16: 56,257,939		probably benign	Het
Iqcf3	A	G	9: 106,560,949		probably null	Het
Kcna4	G	A	2: 107,296,543	V541M	probably damaging	Het
Kcnj11	T	C	7: 46,099,816	T28A	probably benign	Het
Kcnmb2	T	A	3: 32,181,867	N88K	probably damaging	Het
Krt2	T	C	15: 101,813,960	E430G	probably damaging	Het
Lins1	C	T	7: 66,710,641	L384F	possibly damaging	Het
Man1c1	G	C	4: 134,703,438	P11R	probably damaging	Het
Mfge8	T	C	7: 79,134,525	N389D	probably damaging	Het
Mug1	C	T	6: 121,884,254	T1278I	probably benign	Het
Myh9	T	C	15: 77,807,877	M161V	probably damaging	Het
Myl7	T	A	11: 5,898,171	Y61F	probably benign	Het
Nlrp4d	A	T	7: 10,362,779		unknown	Het
Nol3	A	G	8: 105,281,933		probably null	Het
Nup85	T	A	11: 115,577,925		probably null	Het
Obscn	T	A	11: 59,012,742	T7619S	probably damaging	Het
Olfr1298	T	C	2: 111,645,881	M39V	probably benign	Het
Olfr331	T	A	11: 58,501,668	N296I	probably damaging	Het
Olfr628	C	T	7: 103,732,250	T108I	possibly damaging	Het
Olfr844	G	A	9: 19,318,845	V104I	probably benign	Het
Pax5	T	A	4: 44,679,494	I184F	probably damaging	Het
Pcdha7	T	A	18: 36,974,507	V195D	probably damaging	Het
Phf3	A	T	1: 30,813,939		probably benign	Het
Pla2g15	G	T	8: 106,163,071	G325V	probably damaging	Het
Ppp1r21	T	C	17: 88,572,615	F487L	probably benign	Het
Ppp1r9a	A	G	6: 5,157,016	I965V	probably benign	Het
Ptpru	A	G	4: 131,820,964	V74A	probably damaging	Het
Rif1	T	A	2: 52,098,934	Y780N	probably damaging	Het
Rps25	T	A	9: 44,408,749	Y23N	possibly damaging	Het
Ryr1	T	C	7: 29,085,833	D1811G	probably damaging	Het
Scamp5	T	G	9: 57,452,036		probably null	Het
Senp1	T	C	15: 98,045,896	D602G	probably damaging	Het
Sh2b2	T	G	5: 136,231,957	D135A	probably damaging	Het
Slc26a8	G	A	17: 28,638,661	T836M	probably benign	Het
Slfn4	T	G	11: 83,186,821	I145S	possibly damaging	Het
Spag6l	G	A	16: 16,777,390	T377I	probably benign	Het
Spdye4b	T	C	5: 143,196,334	F129S	probably damaging	Het
Sspo	G	A	6: 48,470,580	G2360E	probably benign	Het
Taar2	A	T	10: 23,940,771	I70F	probably damaging	Het
Taar7e	A	G	10: 24,038,566	N318S	probably damaging	Het
Tor1a	C	A	2: 30,967,730	R42L	probably benign	Het
Trdn	A	T	10: 33,474,506	Q690H	probably benign	Het
Trim56	C	A	5: 137,112,725	V646L	probably benign	Het
Tspan15	T	A	10: 62,191,544	K165I	probably benign	Het
Usp24	A	G	4: 106,416,048	Y2210C	probably damaging	Het
Usp45	A	G	4: 21,797,307	T76A	probably damaging	Het
Vps13c	T	A	9: 67,878,224		probably null	Het
Zfp512b	T	C	2: 181,585,095		probably benign	Het
Zyx	C	A	6: 42,356,159		probably null	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
R0220:Kdm2a	UTSW	19	4324919	missense	possibly damaging	0.85
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
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'- AATATCAAGGTGCACATAGAAGCCC -3'
(R):5'- AAAGAGCTCCACGGGACATC -3'

Sequencing Primer
(F):5'- GTGCACATAGAAGCCCTGTCAC -3'
(R):5'- GACATCCATTGTGCCCAAGCTG -3'

Posted On

2015-12-21