Mutagenetix > Incidental Mutation

Incidental Mutation 'R2207:Kdm2a'

239200

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

040209-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.966) question?

Stock #

R2207 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

4366172-4448749 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 4412898 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 29 (D29E)

Ref Sequence

ENSEMBL: ENSMUSP00000139651 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047898] [ENSMUST00000075856] [ENSMUST00000116571] [ENSMUST00000175959]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047898
AA Change: D29E

PolyPhen 2 Score 0.934 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: D29E

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: D29E

PolyPhen 2 Score 0.934 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: D29E

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 damaging
Transcript: ENSMUST00000116571
AA Change: D29E

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000139651
Gene: ENSMUSG00000054611
AA Change: D29E

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	5.9e-37	SMART
low complexity region	416	433	N/A	INTRINSIC
PDB:2YU2\|A	440	493	4e-21	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175682

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175777

Predicted Effect

possibly damaging
Transcript: ENSMUST00000175959
AA Change: D6E

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

SMART Domains

Protein: ENSMUSP00000135689
Gene: ENSMUSG00000054611
AA Change: D6E

Domain	Start	End	E-Value	Type
PDB:2YU2\|A	1	206	1e-140	PDB
Blast:JmjC	7	79	8e-23	BLAST
Blast:JmjC	125	206	3e-55	BLAST

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.5%
20x: 95.9%

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: 99 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410137M14Rik	A	G	17: 37,288,965 (GRCm39)		probably benign	Het
Abcb1b	C	T	5: 8,874,803 (GRCm39)	R488C	probably benign	Het
Adam34	T	C	8: 44,105,274 (GRCm39)	I124V	probably benign	Het
Aicda	T	A	6: 122,538,244 (GRCm39)	V134D	possibly damaging	Het
Akt2	T	A	7: 27,336,625 (GRCm39)		probably null	Het
Aldh1a3	T	C	7: 66,055,769 (GRCm39)	R341G	probably damaging	Het
Ankrd12	G	T	17: 66,338,569 (GRCm39)		probably null	Het
Anxa11	A	G	14: 25,874,721 (GRCm39)	Y244C	probably damaging	Het
Atp2c2	G	A	8: 120,475,048 (GRCm39)	R551Q	probably damaging	Het
B4galt3	C	A	1: 171,101,613 (GRCm39)	H196N	probably damaging	Het
Bcl11a	G	T	11: 24,113,343 (GRCm39)	G229W	probably damaging	Het
Brip1	A	G	11: 85,952,703 (GRCm39)	V1026A	probably benign	Het
Cacna1h	A	T	17: 25,603,987 (GRCm39)	S1282T	probably benign	Het
Calcr	T	C	6: 3,717,133 (GRCm39)	Y109C	probably damaging	Het
Ccdc39	T	C	3: 33,890,882 (GRCm39)	I241V	probably damaging	Het
Ccdc9	A	G	7: 16,018,194 (GRCm39)		probably benign	Het
Cdk17	G	A	10: 93,064,624 (GRCm39)	D298N	probably damaging	Het
Cdkl3	A	G	11: 51,918,020 (GRCm39)	*354W	probably null	Het
Celf6	A	T	9: 59,511,610 (GRCm39)	Y401F	possibly damaging	Het
Clec4a4	C	T	6: 122,990,766 (GRCm39)	L169F	probably damaging	Het
Col14a1	T	C	15: 55,327,082 (GRCm39)	F1411L	unknown	Het
Col4a2	G	T	8: 11,493,352 (GRCm39)	G1354W	probably damaging	Het
Crygs	C	T	16: 22,624,301 (GRCm39)	G102D	possibly damaging	Het
Cst13	A	T	2: 148,665,202 (GRCm39)	R66W	probably damaging	Het
Depp1	G	A	6: 116,628,683 (GRCm39)	V9M	possibly damaging	Het
Dhx8	A	G	11: 101,641,797 (GRCm39)	T632A	probably benign	Het
Disp1	A	G	1: 182,869,906 (GRCm39)	F838S	possibly damaging	Het
Dlg1	A	G	16: 31,672,664 (GRCm39)	H599R	probably benign	Het
Dnah12	T	A	14: 26,503,744 (GRCm39)	V1654E	probably damaging	Het
Dnah5	C	T	15: 28,343,817 (GRCm39)	L2406F	probably benign	Het
Fam98b	C	G	2: 117,098,300 (GRCm39)	R257G	probably damaging	Het
Fbn2	A	T	18: 58,214,471 (GRCm39)	C900*	probably null	Het
Fgf1	A	G	18: 38,980,138 (GRCm39)	Y79H	possibly damaging	Het
Foxn1	C	A	11: 78,249,630 (GRCm39)	A632S	probably benign	Het
Fsip2	T	G	2: 82,807,823 (GRCm39)	S1381A	probably benign	Het
Gtf2b	G	A	3: 142,484,081 (GRCm39)	G85D	probably benign	Het
Gyg1	C	A	3: 20,204,703 (GRCm39)	G161C	probably damaging	Het
Hemgn	G	T	4: 46,396,301 (GRCm39)	L312I	possibly damaging	Het
Hic2	T	C	16: 17,075,324 (GRCm39)	M51T	possibly damaging	Het
Hivep2	C	A	10: 14,004,713 (GRCm39)	T437K	probably benign	Het
Hpx	C	T	7: 105,241,633 (GRCm39)	R287H	probably damaging	Het
Igf2bp3	C	T	6: 49,065,488 (GRCm39)	G468E	possibly damaging	Het
Il5ra	C	A	6: 106,689,402 (GRCm39)	E397*	probably null	Het
Itfg1	A	T	8: 86,502,827 (GRCm39)	S246R	probably benign	Het
Lamc2	T	G	1: 153,009,452 (GRCm39)	E784D	possibly damaging	Het
Lrp2	A	T	2: 69,297,372 (GRCm39)	N3196K	possibly damaging	Het
Lyzl1	T	A	18: 4,181,962 (GRCm39)	C96*	probably null	Het
Maf1	A	G	15: 76,236,718 (GRCm39)	T17A	probably benign	Het
Map1b	T	C	13: 99,567,591 (GRCm39)	D1710G	unknown	Het
Megf8	C	T	7: 25,049,222 (GRCm39)	T1773I	probably damaging	Het
Mei1	T	C	15: 81,987,450 (GRCm39)	M414T	probably benign	Het
Myo15a	A	G	11: 60,396,860 (GRCm39)	N2643S	probably benign	Het
Ndufa9	A	G	6: 126,821,772 (GRCm39)	Y64H	probably damaging	Het
Neb	A	T	2: 52,101,579 (GRCm39)	L4354*	probably null	Het
Nom1	T	A	5: 29,644,972 (GRCm39)	I480N	probably damaging	Het
Nrxn3	C	T	12: 89,315,082 (GRCm39)	T331M	probably damaging	Het
Or1a1	G	T	11: 74,087,150 (GRCm39)	V274L	possibly damaging	Het
Or1j16	G	T	2: 36,530,201 (GRCm39)	R50M	possibly damaging	Het
Or4f14b	A	C	2: 111,775,270 (GRCm39)	F177C	probably damaging	Het
Or51a42	A	G	7: 103,708,612 (GRCm39)	S66P	probably damaging	Het
Pcdhb15	A	T	18: 37,608,075 (GRCm39)	T436S	probably benign	Het
Pcdhb18	T	A	18: 37,624,342 (GRCm39)	N557K	probably damaging	Het
Pcdhb6	T	C	18: 37,468,633 (GRCm39)	M518T	probably benign	Het
Pgm2l1	T	A	7: 99,917,319 (GRCm39)		probably null	Het
Pih1d2	C	A	9: 50,532,379 (GRCm39)	H162N	probably benign	Het
Pitrm1	T	A	13: 6,619,327 (GRCm39)	Y721N	probably damaging	Het
Pla2r1	C	A	2: 60,288,779 (GRCm39)	V618F	probably damaging	Het
Plb1	T	C	5: 32,473,984 (GRCm39)	S599P	possibly damaging	Het
Prkg1	T	C	19: 30,556,260 (GRCm39)	D562G	probably damaging	Het
Proser1	T	G	3: 53,385,812 (GRCm39)	S565A	probably benign	Het
Prx	T	A	7: 27,216,213 (GRCm39)	V238E	probably damaging	Het
Psapl1	T	C	5: 36,362,509 (GRCm39)	I367T	probably damaging	Het
Rc3h1	T	C	1: 160,767,595 (GRCm39)	V128A	probably damaging	Het
Rrm1	T	A	7: 102,091,233 (GRCm39)	M1K	probably null	Het
Rsf1	GCG	GCGACG	7: 97,229,114 (GRCm39)		probably benign	Het
Rsl1	A	G	13: 67,330,892 (GRCm39)	T447A	probably benign	Het
Ryr2	A	G	13: 11,825,823 (GRCm39)	S552P	probably damaging	Het
Sbf1	A	G	15: 89,190,896 (GRCm39)	S225P	possibly damaging	Het
Serpina3c	T	A	12: 104,117,757 (GRCm39)	I194F	probably benign	Het
Setd3	C	T	12: 108,073,544 (GRCm39)	V578M	probably benign	Het
Setx	GTGGCT	GT	2: 29,044,073 (GRCm39)	1814	probably null	Het
Slc6a1	T	A	6: 114,285,632 (GRCm39)	V356E	probably damaging	Het
Slfn1	A	G	11: 83,011,992 (GRCm39)	E36G	possibly damaging	Het
Sorcs1	T	C	19: 50,218,655 (GRCm39)	H609R	possibly damaging	Het
Spag16	A	G	1: 70,764,043 (GRCm39)	H621R	probably benign	Het
Spata31d1e	A	G	13: 59,890,920 (GRCm39)	V300A	probably benign	Het
Tg	G	A	15: 66,553,788 (GRCm39)	G401D	probably benign	Het
Tnxb	A	C	17: 34,928,391 (GRCm39)	T2602P	possibly damaging	Het
Trip11	T	C	12: 101,839,701 (GRCm39)	N1643S	probably benign	Het
Ttn	G	A	2: 76,709,687 (GRCm39)	R1581*	probably null	Het
Ttn	A	T	2: 76,796,155 (GRCm39)	I590K	probably benign	Het
Vmn1r225	A	G	17: 20,722,611 (GRCm39)	I17M	possibly damaging	Het
Vmn1r232	A	G	17: 21,134,465 (GRCm39)	L45P	probably benign	Het
Wdr7	T	A	18: 63,910,678 (GRCm39)	V690E	possibly damaging	Het
Xaf1	A	T	11: 72,194,228 (GRCm39)	E36D	possibly damaging	Het
Zfp131	A	T	13: 120,237,348 (GRCm39)	F303I	probably damaging	Het
Zfp513	T	G	5: 31,357,767 (GRCm39)	K202T	probably damaging	Het
Zfp788	A	T	7: 41,299,064 (GRCm39)	I567F	probably damaging	Het
Zfyve26	A	G	12: 79,292,861 (GRCm39)	V2096A	probably damaging	Het

Other mutations in Kdm2a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- ACTTCAAATCTGGCAGAGAATGAG -3'
(R):5'- TGCTTTGGACTAGCAGCTC -3'

Sequencing Primer
(F):5'- CAGGTGATATTTTAACGTTGCACAG -3'
(R):5'- ACTGACTGCTTGGTAGAG -3'

Posted On

2014-10-02