Mutagenetix > Incidental Mutation

Incidental Mutation 'R4824:Kdm2a'

374277

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

042440-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.966) question?

Stock #

R4824 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

4366172-4448749 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 4412815 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 34 (M34T)

Ref Sequence

ENSEMBL: ENSMUSP00000135689 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000047898
AA Change: M57T

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: M57T

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: ENSMUST00000075856
AA Change: M57T

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: M57T

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: M57T

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139651
Gene: ENSMUSG00000054611
AA Change: M57T

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

probably damaging
Transcript: ENSMUST00000175959
AA Change: M34T

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135689
Gene: ENSMUSG00000054611
AA Change: M34T

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

Meta Mutation Damage Score

0.6829

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.8%
20x: 94.0%

Validation Efficiency

98% (123/126)

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: 107 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	G	3: 137,771,437 (GRCm39)	T209A	probably benign	Het
1700086D15Rik	T	C	11: 65,043,441 (GRCm39)		probably benign	Het
A130010J15Rik	G	A	1: 192,856,965 (GRCm39)	V106I	probably benign	Het
Abca16	C	A	7: 120,074,702 (GRCm39)	N580K	possibly damaging	Het
Actrt2	A	T	4: 154,751,344 (GRCm39)	F264Y	probably damaging	Het
Adh4	G	A	3: 138,134,807 (GRCm39)	S327N	possibly damaging	Het
Alkbh5	T	C	11: 60,444,697 (GRCm39)		probably null	Het
Anapc1	T	A	2: 128,470,610 (GRCm39)	T1507S	possibly damaging	Het
Anapc2	A	G	2: 25,167,764 (GRCm39)	R444G	probably damaging	Het
Apoh	G	T	11: 108,305,087 (GRCm39)	W335L	probably benign	Het
B4galt7	A	T	13: 55,752,162 (GRCm39)	H71L	possibly damaging	Het
Bicd2	A	G	13: 49,532,488 (GRCm39)	E358G	probably damaging	Het
Bmper	T	A	9: 23,134,956 (GRCm39)	V7D	possibly damaging	Het
Brca2	T	C	5: 150,463,200 (GRCm39)	F988S	probably damaging	Het
Brix1	A	G	15: 10,485,828 (GRCm39)	V49A	possibly damaging	Het
Brpf3	T	C	17: 29,025,460 (GRCm39)	S178P	probably benign	Het
Btaf1	A	G	19: 36,958,448 (GRCm39)	Y655C	possibly damaging	Het
C1rl	C	G	6: 124,486,040 (GRCm39)	Y470*	probably null	Het
Cacnb4	A	G	2: 52,565,822 (GRCm39)	V21A	probably benign	Het
Caskin1	C	A	17: 24,720,103 (GRCm39)	P437T	probably benign	Het
Casz1	C	A	4: 149,029,028 (GRCm39)	P1158T	probably damaging	Het
Ccdc141	T	A	2: 76,954,680 (GRCm39)	Q189L	probably damaging	Het
Ccr3	T	C	9: 123,828,809 (GRCm39)	V48A	probably damaging	Het
Cebpd	G	A	16: 15,705,978 (GRCm39)	G264S	probably benign	Het
Cert1	C	T	13: 96,752,995 (GRCm39)	P350S	probably benign	Het
Cfap20dc	A	T	14: 8,665,997 (GRCm38)	M1K	probably null	Het
Chd1	C	A	17: 15,953,386 (GRCm39)	S440R	probably damaging	Het
Clip1	T	A	5: 123,769,086 (GRCm39)	E504D	probably damaging	Het
Cmya5	T	C	13: 93,230,082 (GRCm39)	R1669G	probably benign	Het
Col11a2	T	A	17: 34,269,937 (GRCm39)	F456I	probably damaging	Het
Ctnna2	A	T	6: 76,957,764 (GRCm39)	M130K	probably damaging	Het
Elmo2	A	T	2: 165,133,922 (GRCm39)		probably benign	Het
F11	T	C	8: 45,708,379 (GRCm39)	D27G	probably damaging	Het
Faap100	A	T	11: 120,266,412 (GRCm39)		probably null	Het
Fat1	A	G	8: 45,442,151 (GRCm39)	E1151G	probably damaging	Het
Fbll1	T	A	11: 35,688,652 (GRCm39)	I204F	probably damaging	Het
Gle1	T	A	2: 29,830,215 (GRCm39)	V257D	possibly damaging	Het
Hoxc9	T	A	15: 102,890,225 (GRCm39)	C47*	probably null	Het
Hsd17b6	A	G	10: 127,829,524 (GRCm39)	V226A	probably benign	Het
Hsd17b7	C	T	1: 169,788,764 (GRCm39)	R151Q	probably benign	Het
Hsh2d	G	A	8: 72,954,304 (GRCm39)	D229N	probably benign	Het
Ido2	A	G	8: 25,023,875 (GRCm39)	I321T	probably benign	Het
Irf2bp2	T	C	8: 127,318,172 (GRCm39)	T465A	probably benign	Het
Klhl6	C	T	16: 19,775,778 (GRCm39)	R260H	probably damaging	Het
Kntc1	T	A	5: 123,928,196 (GRCm39)	L1231*	probably null	Het
Lca5l	A	C	16: 95,963,229 (GRCm39)	Y412*	probably null	Het
Lipt1	T	C	1: 37,914,513 (GRCm39)	S190P	possibly damaging	Het
Ly6f	T	A	15: 75,143,569 (GRCm39)	V92D	probably damaging	Het
Matn4	T	A	2: 164,235,151 (GRCm39)	M433L	probably benign	Het
Mbtd1	C	A	11: 93,816,528 (GRCm39)	P370T	probably benign	Het
Mcph1	T	A	8: 18,682,703 (GRCm39)		probably null	Het
Muc5b	T	A	7: 141,417,922 (GRCm39)	C3623S	probably damaging	Het
Myt1l	C	A	12: 29,899,399 (GRCm39)	H134N	probably benign	Het
Nav2	A	T	7: 49,058,749 (GRCm39)		probably benign	Het
Ndufaf8	T	C	11: 119,989,992 (GRCm39)	C35R	probably damaging	Het
Neb	G	A	2: 52,094,891 (GRCm39)	T5130I	possibly damaging	Het
Nlrp9c	T	C	7: 26,079,989 (GRCm39)	N624S	possibly damaging	Het
Nr0b2	C	A	4: 133,283,334 (GRCm39)	H190Q	probably damaging	Het
Nrg4	A	G	9: 55,156,405 (GRCm39)		probably benign	Het
Nup88	A	T	11: 70,852,450 (GRCm39)	V215E	probably benign	Het
Oas2	T	G	5: 120,876,411 (GRCm39)	T511P	probably benign	Het
Or1e25	A	G	11: 73,493,426 (GRCm39)	T7A	possibly damaging	Het
Or2t6	A	G	14: 14,175,885 (GRCm38)	S66P	probably damaging	Het
Or5d14	A	C	2: 87,880,432 (GRCm39)	F179V	probably damaging	Het
Or5w8	T	C	2: 87,687,621 (GRCm39)	V34A	probably benign	Het
Or8g26	A	G	9: 39,095,501 (GRCm39)	N9S	probably benign	Het
Or9q1	A	C	19: 13,805,718 (GRCm39)	L14R	probably damaging	Het
Pcdhgb2	T	A	18: 37,823,502 (GRCm39)	N164K	probably damaging	Het
Pde4d	C	G	13: 109,253,400 (GRCm39)	P76A	probably benign	Het
Phlda1	T	C	10: 111,343,516 (GRCm39)		probably benign	Het
Plekhh1	A	G	12: 79,101,577 (GRCm39)	T216A	probably benign	Het
Plppr3	T	A	10: 79,701,507 (GRCm39)	E445V	possibly damaging	Het
Prom1	A	G	5: 44,191,732 (GRCm39)	V337A	probably damaging	Het
Prr14l	T	C	5: 33,001,743 (GRCm39)		probably benign	Het
Psmd1	A	G	1: 86,064,820 (GRCm39)	I951V	probably benign	Het
Rab35	T	G	5: 115,781,454 (GRCm39)	I85M	possibly damaging	Het
Rad9a	A	T	19: 4,250,536 (GRCm39)	S93T	probably benign	Het
Ric1	G	A	19: 29,563,242 (GRCm39)	C555Y	probably damaging	Het
Rnd2	C	T	11: 101,359,825 (GRCm39)	L57F	probably damaging	Het
Ror2	T	A	13: 53,264,719 (GRCm39)	Q791L	probably benign	Het
Rps8	G	C	4: 117,012,352 (GRCm39)		probably benign	Het
Sdr16c5	C	T	4: 4,016,216 (GRCm39)	W70*	probably null	Het
Senp3	A	G	11: 69,568,821 (GRCm39)	V408A	probably benign	Het
Sh2d4b	C	A	14: 40,562,301 (GRCm39)	W288L	probably benign	Het
Slc38a9	A	T	13: 112,859,832 (GRCm39)	D422V	probably damaging	Het
Slc4a2	T	C	5: 24,645,141 (GRCm39)	F1104L	probably damaging	Het
Slc4a3	A	G	1: 75,527,267 (GRCm39)	K113E	possibly damaging	Het
Spata3	G	A	1: 85,952,048 (GRCm39)		probably null	Het
Spata31d1d	A	T	13: 59,877,055 (GRCm39)	V160E	possibly damaging	Het
Sprr2f	A	G	3: 92,273,203 (GRCm39)	M1V	probably null	Het
Sptbn1	A	G	11: 30,068,295 (GRCm39)	V1733A	possibly damaging	Het
Syce1	C	A	7: 140,359,809 (GRCm39)	L83F	probably damaging	Het
Tardbp	A	G	4: 148,702,050 (GRCm39)	I295T	probably benign	Het
Tmem212	A	G	3: 27,939,157 (GRCm39)	S110P	probably damaging	Het
Tnc	G	A	4: 63,935,857 (GRCm39)	Q360*	probably null	Het
Tnrc6c	C	A	11: 117,613,731 (GRCm39)	Q630K	probably damaging	Het
Ttc19	G	A	11: 62,199,922 (GRCm39)	R235H	probably benign	Het
Ube3b	T	A	5: 114,553,787 (GRCm39)		probably null	Het
Vmn2r31	C	T	7: 7,390,062 (GRCm39)		probably null	Het
Vmn2r92	T	A	17: 18,372,183 (GRCm39)		probably benign	Het
Washc5	A	T	15: 59,205,485 (GRCm39)	Y685*	probably null	Het
Wdr93	T	A	7: 79,399,817 (GRCm39)	Y135*	probably null	Het
Wdr95	T	A	5: 149,518,797 (GRCm39)	I546K	probably damaging	Het
Zbtb38	T	A	9: 96,570,254 (GRCm39)	T277S	probably benign	Het
Zfp13	T	C	17: 23,795,797 (GRCm39)	D258G	possibly damaging	Het
Zfp397	T	A	18: 24,093,249 (GRCm39)	S245T	probably benign	Het
Zfp646	T	C	7: 127,482,907 (GRCm39)	Y1695H	probably benign	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
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
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'- ACAGTTTCCTAAGGGTCAAGGC -3'
(R):5'- GCACTGACTGCTTGGTAGAG -3'

Sequencing Primer
(F):5'- CATGTAGCAGAGTCTGGCCTTAAC -3'
(R):5'- CGCTATGAAGATGATGGC -3'

Posted On

2016-03-01