Mutagenetix > Incidental Mutation

Incidental Mutation 'R3788:Kdm2a'

272411

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

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R3788 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

4314419-4398285 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 4351805 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 207 (C207S)

Ref Sequence

ENSEMBL: ENSMUSP00000076698 (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: C207S

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: C207S

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: C207S

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: C207S

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: C207S

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139651
Gene: ENSMUSG00000054611
AA Change: C207S

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: C184S

PolyPhen 2 Score 0.731 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000135689
Gene: ENSMUSG00000054611
AA Change: C184S

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

0.8738

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.1%

Validation Efficiency

100% (61/61)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610507B11Rik	T	A	11: 78,288,297		probably null	Het
Abca4	T	A	3: 122,052,912	V26E	possibly damaging	Het
Abhd16a	A	G	17: 35,101,587	N411S	probably damaging	Het
Akap13	G	A	7: 75,702,153		probably null	Het
Aph1b	T	C	9: 66,794,066		probably benign	Het
Aspm	C	T	1: 139,463,203	T742I	probably damaging	Het
Bclaf3	A	G	X: 159,566,496	H619R	probably benign	Het
Cemip	A	T	7: 83,943,898	L1199H	probably damaging	Het
Chd2	G	A	7: 73,447,130		probably benign	Het
Clnk	A	G	5: 38,714,998	Y310H	probably damaging	Het
Crmp1	A	G	5: 37,284,140	D522G	probably damaging	Het
Cyth3	A	G	5: 143,636,543		probably benign	Het
Dcbld1	T	A	10: 52,319,658	Y392N	probably damaging	Het
Fam60a	A	G	6: 148,926,119	S134P	possibly damaging	Het
Flnc	T	C	6: 29,454,057	F1820L	probably damaging	Het
Galnt18	G	A	7: 111,520,115	R385*	probably null	Het
Gpatch3	C	A	4: 133,575,168	R137S	possibly damaging	Het
Gpc6	C	T	14: 117,624,466	P265S	probably damaging	Het
Harbi1	T	A	2: 91,720,607	D308E	probably benign	Het
Hdhd2	G	A	18: 76,955,187		probably null	Het
Hk1	T	C	10: 62,275,688	K737E	possibly damaging	Het
Hnrnpr	G	A	4: 136,336,313	V345M	probably damaging	Het
Kalrn	T	C	16: 34,220,240	H944R	probably damaging	Het
Kirrel	C	T	3: 87,089,151	M380I	probably null	Het
Krt75	C	T	15: 101,573,521	G104D	possibly damaging	Het
Lnpk	A	T	2: 74,522,263	S358R	probably benign	Het
Map2	A	G	1: 66,416,863	T1512A	probably damaging	Het
March10	T	A	11: 105,397,079	L132F	probably damaging	Het
Mfrp	G	A	9: 44,105,457	W65*	probably null	Het
Mgat5	A	G	1: 127,366,443	D174G	probably benign	Het
Miga2	T	A	2: 30,371,225	Y177*	probably null	Het
Mroh3	T	C	1: 136,185,475	D747G	probably damaging	Het
Muc5b	A	G	7: 141,863,834	T3506A	possibly damaging	Het
Myo7b	G	T	18: 31,974,112	P1277T	possibly damaging	Het
Naaa	C	T	5: 92,272,554		probably null	Het
Ndufs2	T	C	1: 171,235,320	D410G	possibly damaging	Het
Olfr506	T	A	7: 108,613,073	Y255*	probably null	Het
Olfr559	A	G	7: 102,723,487		probably null	Het
Olfr873	A	G	9: 20,300,370	I58V	probably benign	Het
Olfr955	A	G	9: 39,470,069	I219T	probably benign	Het
Osbp	A	T	19: 11,978,921	Y409F	probably benign	Het
Plxnb1	T	A	9: 109,109,287	V1303D	possibly damaging	Het
Prkcg	G	A	7: 3,313,747	D246N	probably damaging	Het
Ranbp17	GCCTGGATACTGACC	GCC	11: 33,219,203		probably benign	Het
Sbf1	G	A	15: 89,299,528	R1261*	probably null	Het
Scn4a	T	C	11: 106,344,274	N341S	probably damaging	Het
Sec61a2	C	A	2: 5,879,625		probably null	Het
Sgcd	T	A	11: 47,355,205	K57*	probably null	Het
Slc12a5	T	C	2: 164,993,775	L861P	probably damaging	Het
Slc6a16	A	G	7: 45,259,962	D184G	probably benign	Het
Snx7	A	G	3: 117,838,990		probably benign	Het
Sptbn2	A	G	19: 4,745,922	I1710V	probably damaging	Het
Sytl2	A	T	7: 90,376,081	I426F	probably benign	Het
Tdp1	A	G	12: 99,891,752		probably benign	Het
Tmem232	C	A	17: 65,382,633	D496Y	possibly damaging	Het
Tomm20l	C	T	12: 71,111,742	A58V	possibly damaging	Het
Ttc26	T	A	6: 38,403,524		probably null	Het
Ttn	T	C	2: 76,945,274	E1854G	unknown	Het
Ttn	A	G	2: 76,974,208	V240A	probably benign	Het
Vmn2r98	A	T	17: 19,080,625	T630S	probably benign	Het
Xrcc1	G	C	7: 24,566,908	A220P	probably benign	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
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'- AGGTAGCCATCTACAATTCTCTTCAC -3'
(R):5'- AAGATATGGTGTGTCATGCCTG -3'

Sequencing Primer
(F):5'- CTTCACATAGAATGGATGATGTCTCC -3'
(R):5'- GCCTACTCTAGTAGCAAATTCAGG -3'

Posted On

2015-03-25