Mutagenetix > Incidental Mutation

Incidental Mutation 'R0309:Kdm4c'

25037

Institutional Source

Beutler Lab

Gene Symbol

Kdm4c

Ensembl Gene

ENSMUSG00000028397

Gene Name

lysine (K)-specific demethylase 4C

Synonyms

Jmjd2c, 2410141F18Rik

MMRRC Submission

038519-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0309 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

74160734-74324097 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 74263804 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 696 (V696A)

Ref Sequence

ENSEMBL: ENSMUSP00000077017 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030102] [ENSMUST00000077851]

AlphaFold

Q8VCD7

Predicted Effect

probably benign
Transcript: ENSMUST00000030102
AA Change: V696A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000030102
Gene: ENSMUSG00000028397
AA Change: V696A

Domain	Start	End	E-Value	Type
JmjN	15	57	9.12e-14	SMART
JmjC	144	310	1.31e-61	SMART
low complexity region	361	374	N/A	INTRINSIC
low complexity region	386	400	N/A	INTRINSIC
PHD	687	745	3.3e-5	SMART
PHD	807	863	8.71e-5	SMART
TUDOR	875	932	2.96e-10	SMART
TUDOR	933	989	2e-7	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000077851
AA Change: V696A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000077017
Gene: ENSMUSG00000028397
AA Change: V696A

Domain	Start	End	E-Value	Type
JmjN	15	57	9.12e-14	SMART
JmjC	144	310	1.31e-61	SMART
low complexity region	361	374	N/A	INTRINSIC
low complexity region	386	400	N/A	INTRINSIC
PHD	687	745	3.3e-5	SMART
PHD	807	863	8.71e-5	SMART
TUDOR	875	932	2.96e-10	SMART
TUDOR	933	989	2e-7	SMART

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 98.7%
3x: 97.6%
10x: 94.3%
20x: 86.4%

Validation Efficiency

98% (125/127)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Jumonji domain 2 (JMJD2) family. The encoded protein is a trimethylation-specific demethylase, and converts specific trimethylated histone residues to the dimethylated form. This enzymatic action regulates gene expression and chromosome segregation. Chromosomal aberrations and changes in expression of this gene may be found in tumor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
PHENOTYPE: Mice homozygous for a null gene trap allele cannot be produced likely due to embryonic lethality. Mice heterozygous for a null gene trap allele exhibit reduced body weight and lower incidence and multiplicity of both benign and malignant tumors in mice treated with DMBA and TPA. [provided by MGI curators]

Allele List at MGI

All alleles(402) : Targeted, other(2) Gene trapped(400)

Other mutations in this stock

Total: 126 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930402F06Rik	T	C	2: 35,266,271 (GRCm39)	D133G	possibly damaging	Het
Abcb4	A	C	5: 8,989,835 (GRCm39)	D796A	probably damaging	Het
Actg2	A	T	6: 83,496,896 (GRCm39)	V147E	probably damaging	Het
Adamts13	A	C	2: 26,877,001 (GRCm39)	T534P	probably damaging	Het
Ago1	T	C	4: 126,336,959 (GRCm39)	T249A	probably benign	Het
Ahnak	T	A	19: 8,979,859 (GRCm39)	I381N	probably damaging	Het
Akap9	A	G	5: 4,119,038 (GRCm39)	D3515G	probably benign	Het
Angptl3	T	C	4: 98,922,706 (GRCm39)	V249A	probably benign	Het
Ank	A	G	15: 27,567,658 (GRCm39)	T294A	possibly damaging	Het
Ank1	A	T	8: 23,594,825 (GRCm39)	H204L	probably damaging	Het
Apbb2	A	G	5: 66,468,331 (GRCm39)		probably benign	Het
Arhgap28	A	T	17: 68,208,424 (GRCm39)	S15T	probably benign	Het
Aspm	T	C	1: 139,410,249 (GRCm39)		probably benign	Het
Atp1a4	T	C	1: 172,062,554 (GRCm39)	E651G	probably damaging	Het
B3gnt2	A	T	11: 22,786,860 (GRCm39)	F109L	probably damaging	Het
Bpifb4	T	C	2: 153,801,603 (GRCm39)	F575L	probably damaging	Het
Calhm4	A	G	10: 33,920,043 (GRCm39)	W75R	probably damaging	Het
Calr	C	A	8: 85,569,660 (GRCm39)	K322N	probably benign	Het
Ccdc188	T	C	16: 18,037,169 (GRCm39)	S247P	possibly damaging	Het
Cdr1	T	A	X: 60,228,908 (GRCm39)	D86V	unknown	Het
Cep97	C	T	16: 55,745,421 (GRCm39)	V48I	probably damaging	Het
Chaf1b	T	A	16: 93,681,399 (GRCm39)	C6S	probably damaging	Het
Chd3	C	T	11: 69,247,844 (GRCm39)	D920N	probably damaging	Het
Clk1	T	C	1: 58,452,192 (GRCm39)		probably benign	Het
Cntnap3	T	A	13: 64,905,250 (GRCm39)		probably benign	Het
Col12a1	T	A	9: 79,507,293 (GRCm39)		probably null	Het
Col17a1	G	T	19: 47,659,801 (GRCm39)		probably benign	Het
Coq7	T	A	7: 118,128,940 (GRCm39)	I32F	possibly damaging	Het
Cox6a2	A	T	7: 127,805,107 (GRCm39)	F59I	probably damaging	Het
Cpq	A	G	15: 33,594,297 (GRCm39)	D436G	probably damaging	Het
Ctso	G	A	3: 81,852,168 (GRCm39)		probably null	Het
Cxadr	A	T	16: 78,131,836 (GRCm39)	H274L	probably benign	Het
Cyp2c40	A	T	19: 39,766,495 (GRCm39)	C367S	possibly damaging	Het
Cyp2c70	T	G	19: 40,149,115 (GRCm39)	M344L	possibly damaging	Het
Defa35	G	A	8: 21,555,871 (GRCm39)	V77I	probably benign	Het
Dhx57	A	G	17: 80,582,310 (GRCm39)	Y432H	probably damaging	Het
Dhx9	A	T	1: 153,341,441 (GRCm39)	D601E	probably benign	Het
Dnah7a	C	G	1: 53,444,849 (GRCm39)	D3952H	probably damaging	Het
Dnah9	C	A	11: 65,917,798 (GRCm39)		probably benign	Het
Dstyk	C	A	1: 132,384,602 (GRCm39)		probably benign	Het
Efcab2	T	A	1: 178,303,469 (GRCm39)		probably benign	Het
Ehbp1l1	T	C	19: 5,770,598 (GRCm39)	E287G	possibly damaging	Het
Epgn	A	G	5: 91,180,073 (GRCm39)	T87A	probably benign	Het
Erc2	A	C	14: 27,863,182 (GRCm39)	E803A	probably damaging	Het
Fer	A	G	17: 64,446,011 (GRCm39)	*454W	probably null	Het
Glyr1	T	C	16: 4,849,836 (GRCm39)	D179G	probably damaging	Het
Gm12830	T	A	4: 114,702,173 (GRCm39)		probably benign	Het
Gm9922	C	A	14: 101,967,129 (GRCm39)		probably benign	Het
Gsta3	C	T	1: 21,335,118 (GRCm39)	P200S	possibly damaging	Het
Hmgxb3	G	A	18: 61,288,200 (GRCm39)		probably benign	Het
Hsh2d	G	A	8: 72,954,304 (GRCm39)	D229N	probably benign	Het
Il16	T	C	7: 83,371,762 (GRCm39)	K15E	probably damaging	Het
Kcnip2	T	A	19: 45,782,514 (GRCm39)		probably benign	Het
Kdr	A	G	5: 76,107,587 (GRCm39)		probably benign	Het
Klhl33	T	G	14: 51,128,868 (GRCm39)	H787P	probably damaging	Het
Klk14	A	T	7: 43,343,769 (GRCm39)	T159S	probably benign	Het
Lancl2	A	G	6: 57,680,117 (GRCm39)	N16D	probably damaging	Het
Lemd3	T	C	10: 120,773,015 (GRCm39)	N583S	possibly damaging	Het
Map3k4	TGCTGGCTTCAGGGCCACAGTCCGCTG	TGCTG	17: 12,489,902 (GRCm39)		probably null	Het
Mpl	T	G	4: 118,303,235 (GRCm39)		probably benign	Het
Myh7b	T	C	2: 155,472,592 (GRCm39)		probably benign	Het
Mylk	A	C	16: 34,732,667 (GRCm39)		probably benign	Het
Myof	A	T	19: 37,969,714 (GRCm39)	M316K	probably benign	Het
Nfib	T	A	4: 82,214,974 (GRCm39)	N543I	probably damaging	Het
Nfix	A	G	8: 85,448,403 (GRCm39)	S375P	probably damaging	Het
Nkrf	T	C	X: 36,153,769 (GRCm39)	Q171R	probably damaging	Het
Nmnat2	T	A	1: 152,952,747 (GRCm39)		probably benign	Het
Npffr2	G	A	5: 89,731,206 (GRCm39)	E379K	probably benign	Het
Npr2	T	C	4: 43,640,904 (GRCm39)		probably benign	Het
Nup98	A	C	7: 101,801,635 (GRCm39)	D212E	probably null	Het
Nwd2	T	C	5: 63,964,561 (GRCm39)	Y1382H	probably damaging	Het
Ocstamp	T	C	2: 165,237,912 (GRCm39)	R451G	possibly damaging	Het
Or52s1	T	A	7: 102,861,928 (GRCm39)	I287K	probably damaging	Het
Or6c6c	A	G	10: 129,541,008 (GRCm39)	D87G	probably benign	Het
Pabpc1	C	T	15: 36,597,737 (GRCm39)	A551T	possibly damaging	Het
Pard3	A	T	8: 128,103,378 (GRCm39)		probably benign	Het
Pcdhb12	G	T	18: 37,569,174 (GRCm39)	V107L	probably benign	Het
Pik3cd	A	T	4: 149,747,677 (GRCm39)	V22D	probably damaging	Het
Pkd1l2	A	G	8: 117,724,315 (GRCm39)	V2396A	probably damaging	Het
Pnpla7	T	C	2: 24,877,207 (GRCm39)	I167T	probably damaging	Het
Pphln1	A	T	15: 93,339,588 (GRCm39)	H114L	possibly damaging	Het
Ppm1h	A	G	10: 122,756,687 (GRCm39)	N444S	probably damaging	Het
Prdm9	G	A	17: 15,777,646 (GRCm39)	T146I	probably damaging	Het
Prrc2a	A	G	17: 35,369,891 (GRCm39)		probably benign	Het
Prrx1	T	C	1: 163,140,128 (GRCm39)	D26G	possibly damaging	Het
Ptpn5	T	C	7: 46,729,042 (GRCm39)	E495G	probably damaging	Het
Rab23	A	C	1: 33,773,942 (GRCm39)		probably null	Het
Ralgps1	C	T	2: 33,047,935 (GRCm39)	M348I	probably benign	Het
Ranbp2	A	G	10: 58,315,690 (GRCm39)	T2137A	probably benign	Het
Rapgef4	G	T	2: 72,056,374 (GRCm39)	G654V	probably benign	Het
Rc3h2	A	T	2: 37,269,020 (GRCm39)		probably benign	Het
Reg2	G	A	6: 78,383,169 (GRCm39)	A39T	possibly damaging	Het
Sema4d	C	A	13: 51,879,347 (GRCm39)	V7F	probably benign	Het
Sgip1	T	C	4: 102,772,354 (GRCm39)		probably benign	Het
Sgpl1	C	T	10: 60,949,216 (GRCm39)		probably null	Het
Shisa9	G	A	16: 11,814,987 (GRCm39)	V212M	probably damaging	Het
Shq1	G	A	6: 100,550,588 (GRCm39)	P450L	probably benign	Het
Sin3a	A	G	9: 57,018,196 (GRCm39)	T872A	probably benign	Het
Sipa1l3	C	T	7: 29,047,775 (GRCm39)	R1371Q	probably benign	Het
Skint8	T	C	4: 111,796,064 (GRCm39)	V246A	probably benign	Het
Slc22a20	A	T	19: 6,022,985 (GRCm39)	V386D	probably damaging	Het
Slc28a2b	A	T	2: 122,348,034 (GRCm39)	T253S	probably benign	Het
Slc2a7	G	A	4: 150,242,528 (GRCm39)		probably benign	Het
Slc35a2	T	A	X: 7,755,901 (GRCm39)	Y48N	probably damaging	Het
Slc4a2	G	T	5: 24,639,344 (GRCm39)	S413I	probably damaging	Het
Sntg2	T	C	12: 30,276,772 (GRCm39)	T427A	probably benign	Het
Soat1	T	C	1: 156,270,023 (GRCm39)	Y132C	probably damaging	Het
Stn1	G	T	19: 47,490,112 (GRCm39)	H342N	probably benign	Het
Tarbp1	T	A	8: 127,165,667 (GRCm39)		probably benign	Het
Tas2r113	A	C	6: 132,870,341 (GRCm39)	K123T	probably damaging	Het
Tbck	C	T	3: 132,440,168 (GRCm39)	Q504*	probably null	Het
Tenm3	C	T	8: 48,794,069 (GRCm39)	C380Y	probably damaging	Het
Tent4a	A	T	13: 69,648,051 (GRCm39)	V781E	possibly damaging	Het
Triobp	A	G	15: 78,860,740 (GRCm39)	D1389G	probably damaging	Het
Trpm4	A	T	7: 44,958,130 (GRCm39)	F780I	probably damaging	Het
Tubb4a	G	T	17: 57,388,182 (GRCm39)	Y281*	probably null	Het
Txndc15	T	C	13: 55,872,395 (GRCm39)	F261S	probably damaging	Het
Ube3b	T	C	5: 114,557,530 (GRCm39)		probably benign	Het
Unc5c	G	C	3: 141,439,694 (GRCm39)	V196L	probably benign	Het
Upf3a	G	A	8: 13,845,500 (GRCm39)		probably null	Het
Vmn2r20	T	C	6: 123,363,063 (GRCm39)	K574E	probably benign	Het
Vps50	A	G	6: 3,536,853 (GRCm39)	M275V	possibly damaging	Het
Xrcc5	A	G	1: 72,346,735 (GRCm39)		probably benign	Het
Zbtb18	T	C	1: 177,276,182 (GRCm39)	L505S	probably damaging	Het
Zbtb41	T	C	1: 139,366,722 (GRCm39)	I567T	probably damaging	Het
Zfp598	T	C	17: 24,897,558 (GRCm39)		probably benign	Het

Other mutations in Kdm4c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00093:Kdm4c	APN	4	74,263,738 (GRCm39)	missense	probably benign	0.19
IGL00225:Kdm4c	APN	4	74,263,804 (GRCm39)	missense	probably benign	0.03
IGL00672:Kdm4c	APN	4	74,261,751 (GRCm39)	missense	probably benign	0.00
IGL00897:Kdm4c	APN	4	74,291,921 (GRCm39)	missense	probably damaging	1.00
IGL01479:Kdm4c	APN	4	74,261,738 (GRCm39)	missense	probably benign	0.18
IGL01707:Kdm4c	APN	4	74,255,164 (GRCm39)	missense	probably damaging	1.00
IGL02142:Kdm4c	APN	4	74,225,253 (GRCm39)	critical splice donor site	probably null
IGL02268:Kdm4c	APN	4	74,291,953 (GRCm39)	missense	possibly damaging	0.94
IGL02662:Kdm4c	APN	4	74,323,058 (GRCm39)	missense	probably damaging	0.99
IGL03377:Kdm4c	APN	4	74,189,492 (GRCm39)	missense	possibly damaging	0.82
3-1:Kdm4c	UTSW	4	74,252,910 (GRCm39)	missense	probably benign	0.00
BB002:Kdm4c	UTSW	4	74,323,058 (GRCm39)	missense	probably damaging	0.99
BB012:Kdm4c	UTSW	4	74,323,058 (GRCm39)	missense	probably damaging	0.99
PIT4434001:Kdm4c	UTSW	4	74,189,569 (GRCm39)	missense	probably benign	0.01
R0096:Kdm4c	UTSW	4	74,275,580 (GRCm39)	missense	probably damaging	1.00
R0096:Kdm4c	UTSW	4	74,275,580 (GRCm39)	missense	probably damaging	1.00
R0219:Kdm4c	UTSW	4	74,291,857 (GRCm39)	missense	probably damaging	1.00
R0512:Kdm4c	UTSW	4	74,252,031 (GRCm39)	missense	probably benign
R1070:Kdm4c	UTSW	4	74,291,865 (GRCm39)	nonsense	probably null
R1518:Kdm4c	UTSW	4	74,252,063 (GRCm39)	missense	probably benign
R1713:Kdm4c	UTSW	4	74,216,721 (GRCm39)	missense	probably benign	0.10
R1769:Kdm4c	UTSW	4	74,199,234 (GRCm39)	missense	possibly damaging	0.66
R1927:Kdm4c	UTSW	4	74,263,720 (GRCm39)	missense	probably benign	0.00
R1962:Kdm4c	UTSW	4	74,225,253 (GRCm39)	intron	probably benign
R1992:Kdm4c	UTSW	4	74,261,631 (GRCm39)	missense	possibly damaging	0.71
R2389:Kdm4c	UTSW	4	74,252,107 (GRCm39)	critical splice donor site	probably null
R2979:Kdm4c	UTSW	4	74,291,965 (GRCm39)	nonsense	probably null
R3966:Kdm4c	UTSW	4	74,216,820 (GRCm39)	missense	probably damaging	1.00
R4094:Kdm4c	UTSW	4	74,229,915 (GRCm39)	missense	probably benign
R4171:Kdm4c	UTSW	4	74,199,135 (GRCm39)	missense	possibly damaging	0.73
R4543:Kdm4c	UTSW	4	74,248,997 (GRCm39)	missense	probably benign	0.01
R4581:Kdm4c	UTSW	4	74,275,576 (GRCm39)	splice site	probably null
R5019:Kdm4c	UTSW	4	74,261,772 (GRCm39)	missense	probably damaging	1.00
R5088:Kdm4c	UTSW	4	74,252,936 (GRCm39)	missense	probably benign
R5533:Kdm4c	UTSW	4	74,233,886 (GRCm39)	intron	probably benign
R5663:Kdm4c	UTSW	4	74,317,585 (GRCm39)	missense	probably damaging	1.00
R5691:Kdm4c	UTSW	4	74,252,965 (GRCm39)	missense	probably benign
R5775:Kdm4c	UTSW	4	74,277,668 (GRCm39)	missense	probably damaging	1.00
R5786:Kdm4c	UTSW	4	74,277,722 (GRCm39)	missense	probably damaging	0.98
R6002:Kdm4c	UTSW	4	74,323,206 (GRCm39)	missense	possibly damaging	0.95
R6375:Kdm4c	UTSW	4	74,248,952 (GRCm39)	missense	probably damaging	0.96
R6491:Kdm4c	UTSW	4	74,291,873 (GRCm39)	missense	probably damaging	1.00
R6790:Kdm4c	UTSW	4	74,309,698 (GRCm39)	missense	probably damaging	1.00
R6952:Kdm4c	UTSW	4	74,275,587 (GRCm39)	missense	probably damaging	1.00
R7157:Kdm4c	UTSW	4	74,263,804 (GRCm39)	missense	probably benign	0.01
R7319:Kdm4c	UTSW	4	74,255,200 (GRCm39)	missense	probably damaging	1.00
R7925:Kdm4c	UTSW	4	74,323,058 (GRCm39)	missense	probably damaging	0.99
R7976:Kdm4c	UTSW	4	74,295,906 (GRCm39)	missense	probably damaging	0.99
R7990:Kdm4c	UTSW	4	74,309,685 (GRCm39)	missense	probably damaging	1.00
R8185:Kdm4c	UTSW	4	74,291,821 (GRCm39)	missense	probably benign	0.01
R9079:Kdm4c	UTSW	4	74,277,738 (GRCm39)	missense	probably benign	0.01
R9486:Kdm4c	UTSW	4	74,252,966 (GRCm39)	missense	probably benign	0.00
R9546:Kdm4c	UTSW	4	74,323,104 (GRCm39)	missense	possibly damaging	0.90
R9547:Kdm4c	UTSW	4	74,323,104 (GRCm39)	missense	possibly damaging	0.90

Predicted Primers

PCR Primer
(F):5'- ACATGTGGATCACAGATGTATGTGAGC -3'
(R):5'- CAAAGGAACTGACAGGTTACTCTGAGG -3'

Sequencing Primer
(F):5'- GAACTCTTGTATGAACTCTCAGAGC -3'
(R):5'- ACTCTGAGGTGATTTGTAAGGGC -3'

Posted On

2013-04-16