Mutagenetix > Incidental Mutation

Incidental Mutation 'R4838:Kdm2a'

371585

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

Accession Numbers

Essential gene?

Probably essential (E-score: 0.966) question?

Stock #

R4838 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

4366172-4448749 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 4375054 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 692 (S692R)

Ref Sequence

ENSEMBL: ENSMUSP00000076698 (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
AA Change: S692R

PolyPhen 2 Score 0.413 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000047683
Gene: ENSMUSG00000054611
AA Change: S692R

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
AA Change: S692R

PolyPhen 2 Score 0.413 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000076698
Gene: ENSMUSG00000054611
AA Change: S692R

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
AA Change: S252R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000135745
Gene: ENSMUSG00000054611
AA Change: S252R

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: 98.5%
10x: 96.9%
20x: 94.0%

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	T	C	7: 119,944,523 (GRCm39)	V386A	probably benign	Het
Adk	G	A	14: 21,419,154 (GRCm39)	A247T	probably damaging	Het
Ankrd27	T	A	7: 35,291,231 (GRCm39)	L9Q	possibly damaging	Het
Atad2	A	G	15: 57,966,679 (GRCm39)	L638P	probably damaging	Het
Atf7ip	T	A	6: 136,573,489 (GRCm39)	D1009E	probably benign	Het
Bend7	A	T	2: 4,749,133 (GRCm39)	K83N	probably damaging	Het
Bicc1	C	T	10: 70,781,146 (GRCm39)	D562N	possibly damaging	Het
Calcrl	T	A	2: 84,181,549 (GRCm39)	N200Y	probably damaging	Het
Ccdc125	C	A	13: 100,814,453 (GRCm39)	A11E	possibly damaging	Het
Cd5l	A	G	3: 87,273,258 (GRCm39)	T76A	probably benign	Het
Cdhr5	A	T	7: 140,853,644 (GRCm39)	I2N	probably damaging	Het
Cdk10	C	T	8: 123,957,353 (GRCm39)	A230V	probably damaging	Het
Cep128	T	C	12: 90,966,319 (GRCm39)		probably benign	Het
Cep131	T	C	11: 119,966,982 (GRCm39)	N186D	probably damaging	Het
Cfhr4	T	A	1: 139,661,181 (GRCm39)	D556V	probably damaging	Het
Cog7	G	T	7: 121,570,604 (GRCm39)	P168Q	probably damaging	Het
Col28a1	T	A	6: 8,014,559 (GRCm39)	M949L	probably benign	Het
Coq8b	T	A	7: 26,950,016 (GRCm39)	M365K	probably damaging	Het
Cpa1	A	G	6: 30,639,515 (GRCm39)	E18G	possibly damaging	Het
Csmd2	A	G	4: 128,411,542 (GRCm39)	H2520R	probably benign	Het
Cyp2c69	T	C	19: 39,866,038 (GRCm39)	N185S	probably benign	Het
Dpm1	G	A	2: 168,052,456 (GRCm39)	T260I	probably damaging	Het
Dtx3	A	T	10: 127,027,176 (GRCm39)		probably null	Het
Eepd1	T	C	9: 25,500,756 (GRCm39)	V401A	possibly damaging	Het
Ehhadh	A	G	16: 21,581,952 (GRCm39)	S347P	possibly damaging	Het
Elp3	A	G	14: 65,785,313 (GRCm39)		probably null	Het
Enam	C	T	5: 88,640,967 (GRCm39)	Q210*	probably null	Het
Epha1	C	T	6: 42,340,750 (GRCm39)	R607H	probably benign	Het
Erich6	A	G	3: 58,544,251 (GRCm39)	I112T	probably benign	Het
F830045P16Rik	A	G	2: 129,302,470 (GRCm39)	V374A	possibly damaging	Het
Fam171a2	C	A	11: 102,329,511 (GRCm39)	R416L	possibly damaging	Het
Fbn1	T	C	2: 125,214,319 (GRCm39)	N764S	probably benign	Het
Fip1l1	C	T	5: 74,752,600 (GRCm39)	T469I	probably damaging	Het
Flad1	G	A	3: 89,313,217 (GRCm39)	R342C	probably damaging	Het
Fzd3	A	G	14: 65,477,269 (GRCm39)	V95A	probably benign	Het
Garem1	T	C	18: 21,280,950 (GRCm39)	T469A	probably benign	Het
Gm17093	A	G	14: 44,755,805 (GRCm39)	Y24C	unknown	Het
Grap2	T	C	15: 80,522,762 (GRCm39)	V96A	possibly damaging	Het
Greb1	A	T	12: 16,734,361 (GRCm39)		probably null	Het
Grid2ip	A	T	5: 143,374,530 (GRCm39)	K913*	probably null	Het
Gzmk	T	C	13: 113,309,555 (GRCm39)	D126G	probably damaging	Het
Hibch	A	G	1: 52,924,337 (GRCm39)	I171V	possibly damaging	Het
Hipk2	G	T	6: 38,795,339 (GRCm39)	T310K	possibly damaging	Het
Hk3	T	C	13: 55,154,231 (GRCm39)	Y815C	probably damaging	Het
Hps5	A	T	7: 46,437,778 (GRCm39)	V99E	probably damaging	Het
Hspg2	A	G	4: 137,268,977 (GRCm39)	H2203R	possibly damaging	Het
Il12rb2	A	G	6: 67,286,121 (GRCm39)	V108A	probably damaging	Het
Il6st	C	T	13: 112,627,044 (GRCm39)	R279*	probably null	Het
Kif13a	T	C	13: 46,980,224 (GRCm39)	K176R	probably damaging	Het
Kif5b	T	C	18: 6,216,869 (GRCm39)	K485E	probably damaging	Het
Ktn1	C	T	14: 47,963,413 (GRCm39)	R1111*	probably null	Het
Lrrc23	A	T	6: 124,755,152 (GRCm39)	N128K	probably benign	Het
Mad1l1	G	A	5: 140,286,017 (GRCm39)	Q293*	probably null	Het
Man1b1	A	T	2: 25,235,487 (GRCm39)	I338F	possibly damaging	Het
Marchf1	G	T	8: 66,921,015 (GRCm39)	V225L	probably damaging	Het
Matcap2	A	T	9: 22,335,673 (GRCm39)	D97V	probably damaging	Het
Mrpl3	A	G	9: 104,934,231 (GRCm39)	D118G	probably damaging	Het
Nomo1	A	T	7: 45,733,139 (GRCm39)	Q1209L	unknown	Het
Nrcam	A	G	12: 44,620,802 (GRCm39)	E949G	probably damaging	Het
Olfm5	T	G	7: 103,803,572 (GRCm39)	N297T	probably damaging	Het
Or51h7	T	A	7: 102,591,453 (GRCm39)	L110F	probably damaging	Het
Pcdh7	A	T	5: 57,878,146 (GRCm39)	N567I	probably damaging	Het
Pkn1	A	G	8: 84,404,595 (GRCm39)	L495P	probably damaging	Het
Pkp1	T	C	1: 135,810,326 (GRCm39)	S415G	probably damaging	Het
Pou2f1	T	A	1: 165,744,492 (GRCm39)	Q53L	probably null	Het
Pramel26	G	A	4: 143,537,375 (GRCm39)	Q319*	probably null	Het
Prkce	A	G	17: 86,937,511 (GRCm39)	K648R	probably benign	Het
Ptprh	G	A	7: 4,576,429 (GRCm39)	T277I	possibly damaging	Het
Rpl31	C	T	1: 39,410,048 (GRCm39)	R83C	probably benign	Het
Rpusd3	G	A	6: 113,393,837 (GRCm39)	Q194*	probably null	Het
Sgsm1	T	A	5: 113,430,492 (GRCm39)	N298Y	probably damaging	Het
She	G	A	3: 89,758,946 (GRCm39)	G355D	probably benign	Het
Shld2	A	G	14: 33,990,582 (GRCm39)	V108A	probably benign	Het
Snx11	C	T	11: 96,665,284 (GRCm39)	E9K	possibly damaging	Het
Soat1	C	A	1: 156,260,507 (GRCm39)	A444S	probably benign	Het
Sox6	T	C	7: 115,085,897 (GRCm39)	Y690C	probably damaging	Het
Spata13	T	A	14: 60,970,628 (GRCm39)	F10I	probably benign	Het
St18	C	A	1: 6,873,129 (GRCm39)	T288K	probably benign	Het
Tifa	C	T	3: 127,590,235 (GRCm39)	S2F	probably damaging	Het
Tmem232	A	T	17: 65,737,883 (GRCm39)	S392R	probably benign	Het
Tmtc3	T	C	10: 100,302,082 (GRCm39)	N289S	probably damaging	Het
Tpo	A	G	12: 30,142,633 (GRCm39)	F697S	probably damaging	Het
Trp53	A	G	11: 69,478,456 (GRCm39)	T122A	probably damaging	Het
Trps1	A	C	15: 50,690,712 (GRCm39)	I10S	probably benign	Het
Tubgcp5	C	T	7: 55,443,933 (GRCm39)		probably benign	Het
Unc13c	T	G	9: 73,839,354 (GRCm39)	Y499S	possibly damaging	Het
Unc45a	C	A	7: 79,982,783 (GRCm39)	D381Y	probably damaging	Het
Upf1	G	C	8: 70,792,018 (GRCm39)	H402Q	probably benign	Het
Uroc1	A	T	6: 90,326,174 (GRCm39)	I510F	possibly damaging	Het
Usp15	A	G	10: 122,963,662 (GRCm39)	F589L	probably damaging	Het
Vmn2r76	T	C	7: 85,874,733 (GRCm39)	Y748C	probably damaging	Het
Wwp1	T	C	4: 19,662,143 (GRCm39)	N151D	probably benign	Het
Zbtb40	A	T	4: 136,728,527 (GRCm39)	S439T	probably benign	Het
Zbtb6	A	T	2: 37,318,728 (GRCm39)	L400*	probably null	Het
Zfp125	C	T	12: 20,949,961 (GRCm39)		noncoding transcript	Het
Zmynd8	A	C	2: 165,681,954 (GRCm39)	Y183*	probably null	Het
Zpld2	A	G	4: 133,920,410 (GRCm39)	V585A	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
R4824:Kdm2a	UTSW	19	4,412,815 (GRCm39)	missense	probably damaging	1.00
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'- GCCGTTTGAAGCGTTCATC -3'
(R):5'- TTCTATGGCCTGGGTTCACATG -3'

Sequencing Primer
(F):5'- TTCATCACGGCTGGCACTG -3'
(R):5'- CACATGTGAGCTCAGTTGCTGATC -3'

Posted On

2016-03-01