Mutagenetix > Incidental Mutation

Incidental Mutation 'R1769:Kdm4c'

194676

Institutional Source

Beutler Lab

Gene Symbol

Kdm4c

Ensembl Gene

ENSMUSG00000028397

Gene Name

lysine (K)-specific demethylase 4C

Synonyms

Jmjd2c, 2410141F18Rik

MMRRC Submission

039800-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1769 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

74160734-74324097 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 74199234 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 141 (S141G)

Ref Sequence

ENSEMBL: ENSMUSP00000077017 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030102] [ENSMUST00000077851] [ENSMUST00000149295]

AlphaFold

Q8VCD7

Predicted Effect

possibly damaging
Transcript: ENSMUST00000030102
AA Change: S141G

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000030102
Gene: ENSMUSG00000028397
AA Change: S141G

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

possibly damaging
Transcript: ENSMUST00000077851
AA Change: S141G

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000077017
Gene: ENSMUSG00000028397
AA Change: S141G

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: ENSMUST00000149295

SMART Domains

Protein: ENSMUSP00000118728
Gene: ENSMUSG00000028397

Domain	Start	End	E-Value	Type
Pfam:JmjN	17	49	9.4e-14	PFAM
low complexity region	102	115	N/A	INTRINSIC
low complexity region	127	141	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156065

Meta Mutation Damage Score

0.4754

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.3%
20x: 92.5%

Validation Efficiency

100% (91/91)

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A430033K04Rik	A	G	5: 138,644,519 (GRCm39)	I135V	probably benign	Het
Abca1	T	A	4: 53,074,325 (GRCm39)	K1119N	probably damaging	Het
Abcb10	C	T	8: 124,688,791 (GRCm39)	G495D	probably damaging	Het
Abcc9	T	C	6: 142,573,194 (GRCm39)		probably benign	Het
Akap3	A	G	6: 126,842,809 (GRCm39)	E476G	possibly damaging	Het
Aldh3b1	A	G	19: 3,968,740 (GRCm39)	F271S	probably damaging	Het
Alkbh2	C	T	5: 114,262,287 (GRCm39)	E148K	probably damaging	Het
Ascc3	T	C	10: 50,576,586 (GRCm39)	V847A	probably damaging	Het
Best3	A	G	10: 116,859,883 (GRCm39)	N381S	probably benign	Het
Blm	A	T	7: 80,163,118 (GRCm39)	S78T	probably benign	Het
Bmpr2	T	A	1: 59,907,520 (GRCm39)	L871Q	probably damaging	Het
Car13	T	A	3: 14,715,795 (GRCm39)	H104Q	probably benign	Het
Ccdc39	T	C	3: 33,880,629 (GRCm39)	K446R	probably damaging	Het
Ccnb1ip1	T	C	14: 51,029,568 (GRCm39)	M165V	probably benign	Het
Cd4	A	T	6: 124,843,618 (GRCm39)	M431K	possibly damaging	Het
Cdh20	C	T	1: 109,980,606 (GRCm39)	T178I	probably damaging	Het
Ceacam3	C	T	7: 16,892,301 (GRCm39)	T348I	probably damaging	Het
Cfap54	C	T	10: 92,740,125 (GRCm39)		probably null	Het
Clcn6	A	T	4: 148,098,758 (GRCm39)		probably null	Het
Csf3	A	G	11: 98,593,246 (GRCm39)	Y121C	probably damaging	Het
Csmd3	C	T	15: 47,567,505 (GRCm39)		probably benign	Het
Cyp2c69	A	G	19: 39,864,815 (GRCm39)	I221T	probably benign	Het
Dgcr2	T	C	16: 17,675,115 (GRCm39)		probably benign	Het
Dhcr7	T	C	7: 143,401,250 (GRCm39)	F474S	probably damaging	Het
Dnah1	T	C	14: 31,032,839 (GRCm39)	I399V	probably null	Het
Efcab14	T	A	4: 115,610,188 (GRCm39)	L183Q	probably damaging	Het
Evx2	A	G	2: 74,489,501 (GRCm39)	V88A	probably benign	Het
Exph5	A	G	9: 53,285,109 (GRCm39)	N730S	probably benign	Het
Farsb	T	A	1: 78,443,620 (GRCm39)	K196I	probably benign	Het
Fbln7	C	T	2: 128,735,682 (GRCm39)		probably benign	Het
Fhdc1	A	G	3: 84,356,085 (GRCm39)	F453S	probably damaging	Het
Gast	T	A	11: 100,227,684 (GRCm39)	W89R	probably damaging	Het
Gata2	A	G	6: 88,182,237 (GRCm39)	S402G	probably benign	Het
Gin1	T	A	1: 97,720,162 (GRCm39)	S386T	probably benign	Het
Golgb1	A	G	16: 36,736,363 (GRCm39)	E1870G	probably damaging	Het
Hivep3	T	A	4: 119,954,768 (GRCm39)	V1028E	possibly damaging	Het
Ifi203	G	A	1: 173,756,326 (GRCm39)	R486*	probably null	Het
Ifi209	G	A	1: 173,468,728 (GRCm39)	S186N	probably benign	Het
Ifih1	C	T	2: 62,436,738 (GRCm39)	A562T	probably damaging	Het
Itch	T	C	2: 155,014,481 (GRCm39)	L106S	probably damaging	Het
Itga4	T	A	2: 79,146,050 (GRCm39)		probably null	Het
Kirrel1	C	T	3: 86,996,458 (GRCm39)	M380I	probably null	Het
Klra3	T	C	6: 130,307,226 (GRCm39)		probably null	Het
Lama2	G	C	10: 27,084,403 (GRCm39)	F922L	probably benign	Het
Lama2	A	T	10: 27,084,402 (GRCm39)	S923T	probably damaging	Het
Llgl1	G	A	11: 60,597,873 (GRCm39)	V331M	probably damaging	Het
Lrrc30	T	C	17: 67,938,676 (GRCm39)	*301W	probably null	Het
Map1lc3b	C	T	8: 122,320,226 (GRCm39)		probably benign	Het
Mbd2	A	G	18: 70,749,690 (GRCm39)	I302V	probably benign	Het
Med27	A	G	2: 29,390,307 (GRCm39)	Y78C	probably damaging	Het
Mei1	C	T	15: 81,996,771 (GRCm39)		probably null	Het
Mideas	G	A	12: 84,205,124 (GRCm39)		probably benign	Het
Miga1	T	C	3: 151,993,191 (GRCm39)	E346G	probably damaging	Het
Myef2	A	G	2: 124,957,363 (GRCm39)	S131P	probably damaging	Het
Myocd	T	C	11: 65,069,527 (GRCm39)	H899R	probably benign	Het
Ncam1	A	G	9: 49,456,556 (GRCm39)		probably benign	Het
Ngf	T	A	3: 102,427,513 (GRCm39)	N87K	possibly damaging	Het
Nol10	T	A	12: 17,466,709 (GRCm39)		probably benign	Het
Nrip2	A	G	6: 128,385,231 (GRCm39)	I221V	probably benign	Het
Nup205	G	A	6: 35,182,366 (GRCm39)	G777D	probably damaging	Het
Or5ac17	A	G	16: 59,036,344 (GRCm39)	F211L	probably benign	Het
Or5b96	A	G	19: 12,867,047 (GRCm39)	V298A	probably damaging	Het
Or6c1	T	A	10: 129,518,081 (GRCm39)	T176S	probably benign	Het
Or7g35	A	T	9: 19,496,682 (GRCm39)	Q283L	probably damaging	Het
Or8d6	G	T	9: 39,854,251 (GRCm39)	D232Y	probably benign	Het
Oxt	A	T	2: 130,418,220 (GRCm39)	R31W	probably damaging	Het
Pde4dip	A	G	3: 97,603,246 (GRCm39)	S2248P	probably benign	Het
Pias1	A	G	9: 62,859,460 (GRCm39)	V16A	probably damaging	Het
Pkp2	T	C	16: 16,080,561 (GRCm39)	S616P	probably damaging	Het
Plch2	T	C	4: 155,084,540 (GRCm39)	Y379C	probably damaging	Het
Pnpt1	A	G	11: 29,104,159 (GRCm39)	N540D	probably benign	Het
Ptpn23	G	A	9: 110,220,746 (GRCm39)	H255Y	possibly damaging	Het
Rad21	T	C	15: 51,835,703 (GRCm39)	N237D	probably benign	Het
Ryr3	A	C	2: 112,582,113 (GRCm39)		probably null	Het
Sgk1	C	A	10: 21,873,007 (GRCm39)		probably benign	Het
Slc1a5	G	T	7: 16,531,464 (GRCm39)	A490S	probably damaging	Het
Slc5a8	T	C	10: 88,755,326 (GRCm39)	Y478H	probably benign	Het
Slc5a8	T	A	10: 88,755,328 (GRCm39)	Y478*	probably null	Het
Slc9a3	A	T	13: 74,311,190 (GRCm39)	M562L	probably benign	Het
Spmip4	A	G	6: 50,568,801 (GRCm39)		probably benign	Het
Thsd7a	G	A	6: 12,555,714 (GRCm39)	R57*	probably null	Het
Tiam1	T	C	16: 89,657,167 (GRCm39)	R690G	probably damaging	Het
Tmem150b	A	G	7: 4,727,365 (GRCm39)	S47P	probably damaging	Het
Trim39	C	T	17: 36,574,832 (GRCm39)	R190Q	probably damaging	Het
Ttc32	A	T	12: 9,085,073 (GRCm39)	I98L	possibly damaging	Het
Vps13c	A	G	9: 67,873,003 (GRCm39)	T3304A	probably benign	Het
Wdr35	A	C	12: 9,062,728 (GRCm39)	D638A	probably damaging	Het
Wwc1	G	T	11: 35,752,671 (GRCm39)	P797T	probably benign	Het
Zan	T	A	5: 137,462,780 (GRCm39)	T800S	unknown	Het
Zbbx	A	G	3: 74,990,926 (GRCm39)		probably benign	Het
Zup1	T	C	10: 33,811,172 (GRCm39)	M291V	probably damaging	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
R0309:Kdm4c	UTSW	4	74,263,804 (GRCm39)	missense	probably benign	0.00
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
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'- GTTTTGGAAGCCCTACTGATAAGGAACA -3'
(R):5'- cttacccacagatacacaCATGCACATA -3'

Sequencing Primer
(F):5'- CATTAACTCTGATACCACATGAGTG -3'
(R):5'- GAGTACTTCTAAGCTATC -3'

Posted On

2014-05-23