Mutagenetix > Incidental Mutation

Incidental Mutation 'R2979:Kdm4c'

257034

Institutional Source

Beutler Lab

Gene Symbol

Kdm4c

Ensembl Gene

ENSMUSG00000028397

Gene Name

lysine (K)-specific demethylase 4C

Synonyms

Jmjd2c, 2410141F18Rik

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2979 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

74160734-74324097 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

A to T at 74291965 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Stop codon at position 861 (R861*)

Ref Sequence

ENSEMBL: ENSMUSP00000077017 (fasta)

Gene Model

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

AlphaFold

Q8VCD7

Predicted Effect

probably null
Transcript: ENSMUST00000030102
AA Change: R861*

SMART Domains

Protein: ENSMUSP00000030102
Gene: ENSMUSG00000028397
AA Change: R861*

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 null
Transcript: ENSMUST00000077851
AA Change: R861*

SMART Domains

Protein: ENSMUSP00000077017
Gene: ENSMUSG00000028397
AA Change: R861*

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

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.4%

Validation Efficiency

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: 19 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Afm	A	G	5: 90,670,022 (GRCm39)	I48V	probably benign	Het
Arhgef1	A	G	7: 24,607,176 (GRCm39)	E16G	unknown	Het
Cps1	T	C	1: 67,243,863 (GRCm39)		probably null	Het
Dnah9	T	C	11: 66,008,414 (GRCm39)	K804E	possibly damaging	Het
Fabp3	C	T	4: 130,206,180 (GRCm39)	T57I	probably benign	Het
Gm18025	G	T	12: 34,340,970 (GRCm39)	P41Q	probably damaging	Het
Klhl2	C	T	8: 65,275,730 (GRCm39)	V58I	probably damaging	Het
Msl1	G	A	11: 98,691,050 (GRCm39)	G178E	possibly damaging	Het
Nacad	T	A	11: 6,551,424 (GRCm39)	Q589L	probably benign	Het
Pros1	A	G	16: 62,734,229 (GRCm39)	D345G	probably damaging	Het
Sh3tc2	A	G	18: 62,122,556 (GRCm39)	Y439C	probably damaging	Het
Smarcad1	T	A	6: 65,051,995 (GRCm39)	M376K	probably benign	Het
Srd5a1	T	C	13: 69,748,418 (GRCm39)	Q127R	probably damaging	Het
Synm	T	G	7: 67,386,008 (GRCm39)	R551S	probably damaging	Het
Trmt1	A	G	8: 85,423,511 (GRCm39)	Y301C	probably damaging	Het
Ttc23l	G	A	15: 10,537,652 (GRCm39)	S206L	probably benign	Het
Txnl1	T	C	18: 63,804,691 (GRCm39)	T268A	probably benign	Het
Zbbx	C	A	3: 74,985,793 (GRCm39)	E420*	probably null	Het
Zc3h7a	A	T	16: 10,976,837 (GRCm39)	V153E	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
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
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'- GCCCCAGAATCAGAACTTGTG -3'
(R):5'- CTGAATGGTTCTGAGCAACTATG -3'

Sequencing Primer
(F):5'- CCCAGAATCAGAACTTGTGTTGTTC -3'
(R):5'- TGACAGGTCCCAGAAAGA -3'

Posted On

2015-01-11