Mutagenetix > Incidental Mutation

Incidental Mutation 'R0512:Kdm4c'

47884

Institutional Source

Beutler Lab

Gene Symbol

Kdm4c

Ensembl Gene

ENSMUSG00000028397

Gene Name

lysine (K)-specific demethylase 4C

Synonyms

Jmjd2c, 2410141F18Rik

MMRRC Submission

038706-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0512 (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 74252031 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 426 (E426G)

Ref Sequence

ENSEMBL: ENSMUSP00000077017 (fasta)

Gene Model

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

AlphaFold

Q8VCD7

Predicted Effect

probably benign
Transcript: ENSMUST00000030102
AA Change: E426G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000030102
Gene: ENSMUSG00000028397
AA Change: E426G

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: E426G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000077017
Gene: ENSMUSG00000028397
AA Change: E426G

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

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.8%

Validation Efficiency

100% (92/92)

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
4930519G04Rik	T	G	5: 115,001,569 (GRCm39)	M22R	probably benign	Het
Abca8b	C	A	11: 109,841,476 (GRCm39)	M1039I	probably benign	Het
Actn2	A	T	13: 12,292,301 (GRCm39)	I653N	probably damaging	Het
Actr8	G	T	14: 29,700,513 (GRCm39)	V31L	probably benign	Het
Adam30	T	C	3: 98,069,441 (GRCm39)	C425R	probably damaging	Het
Armc1	A	G	3: 19,203,659 (GRCm39)	V89A	possibly damaging	Het
Atr	T	C	9: 95,817,579 (GRCm39)	M2090T	probably damaging	Het
Braf	T	A	6: 39,641,923 (GRCm39)		probably benign	Het
Cant1	A	T	11: 118,302,091 (GRCm39)	N75K	probably benign	Het
Chd7	C	T	4: 8,805,139 (GRCm39)		probably benign	Het
Clec16a	A	G	16: 10,432,444 (GRCm39)	Y488C	probably damaging	Het
Col6a3	A	T	1: 90,749,520 (GRCm39)		probably benign	Het
Col9a2	T	A	4: 120,911,504 (GRCm39)	M615K	probably benign	Het
Dedd	G	A	1: 171,168,498 (GRCm39)	R228H	probably damaging	Het
Dhtkd1	C	T	2: 5,908,902 (GRCm39)	D731N	probably damaging	Het
Ercc2	A	G	7: 19,127,812 (GRCm39)	T651A	probably damaging	Het
Fam13a	T	A	6: 58,933,684 (GRCm39)	D302V	probably damaging	Het
Fam193a	T	C	5: 34,583,735 (GRCm39)	S19P	probably damaging	Het
Fam43a	T	C	16: 30,420,553 (GRCm39)	V379A	possibly damaging	Het
Fat1	C	A	8: 45,404,369 (GRCm39)	Y373*	probably null	Het
Fbxl15	A	C	19: 46,317,861 (GRCm39)	D181A	probably damaging	Het
Flt3	A	T	5: 147,278,080 (GRCm39)	C831*	probably null	Het
Foxj3	T	A	4: 119,443,033 (GRCm39)		probably benign	Het
Glul	T	C	1: 153,781,132 (GRCm39)		probably benign	Het
Gm16380	A	T	9: 53,791,529 (GRCm39)		noncoding transcript	Het
Gm7964	A	T	7: 83,405,158 (GRCm39)		noncoding transcript	Het
Hipk1	A	G	3: 103,667,890 (GRCm39)	F559S	possibly damaging	Het
Hnf4g	A	T	3: 3,716,682 (GRCm39)	I284F	probably damaging	Het
Hoxa13	CCG	CCGCG	6: 52,237,618 (GRCm39)		probably null	Het
Icosl	A	G	10: 77,907,800 (GRCm39)	N120S	possibly damaging	Het
Ift172	A	G	5: 31,442,821 (GRCm39)	V155A	possibly damaging	Het
Kif23	A	G	9: 61,826,257 (GRCm39)		probably benign	Het
Krt81	C	A	15: 101,361,508 (GRCm39)	R24L	possibly damaging	Het
Lama1	G	A	17: 68,086,129 (GRCm39)	C1456Y	possibly damaging	Het
Lamc3	T	A	2: 31,827,980 (GRCm39)	L1378Q	probably damaging	Het
Larp1b	T	A	3: 40,924,469 (GRCm39)	L121M	probably benign	Het
Lepr	T	A	4: 101,649,216 (GRCm39)	D872E	probably damaging	Het
Lepr	A	C	4: 101,671,901 (GRCm39)	D975A	possibly damaging	Het
Magi1	A	G	6: 93,671,045 (GRCm39)	V1068A	probably damaging	Het
Malt1	T	A	18: 65,591,271 (GRCm39)	N358K	probably damaging	Het
Mfap4	T	A	11: 61,378,771 (GRCm39)	W240R	probably damaging	Het
Mis18a	A	G	16: 90,523,244 (GRCm39)	V84A	possibly damaging	Het
Mns1	A	G	9: 72,356,753 (GRCm39)	E308G	possibly damaging	Het
Mpp2	C	A	11: 101,953,116 (GRCm39)	L258F	possibly damaging	Het
Myh2	A	G	11: 67,079,504 (GRCm39)	E987G	probably damaging	Het
Myof	A	G	19: 37,942,972 (GRCm39)	V702A	possibly damaging	Het
Nhs	C	A	X: 160,620,355 (GRCm39)	R1467I	probably damaging	Het
Nrxn2	A	G	19: 6,567,228 (GRCm39)	T1360A	probably damaging	Het
Obox6	A	G	7: 15,567,874 (GRCm39)	I191T	probably benign	Het
Pacs2	G	T	12: 113,014,547 (GRCm39)	R236L	probably damaging	Het
Pcdhb2	T	G	18: 37,429,032 (GRCm39)	V335G	probably damaging	Het
Phyhipl	T	C	10: 70,404,748 (GRCm39)	I140M	probably damaging	Het
Pkhd1	T	C	1: 20,380,738 (GRCm39)		probably benign	Het
Ppp1r3b	T	G	8: 35,851,571 (GRCm39)	C137G	probably damaging	Het
Prdm13	T	A	4: 21,678,490 (GRCm39)	I667F	probably damaging	Het
Prex2	A	G	1: 11,270,157 (GRCm39)	M1281V	probably benign	Het
Rab40b	A	G	11: 121,250,412 (GRCm39)	F81L	probably damaging	Het
Rb1cc1	T	C	1: 6,318,767 (GRCm39)	S729P	probably damaging	Het
Rcl1	A	G	19: 29,105,497 (GRCm39)	D228G	probably damaging	Het
Rhbdf1	A	T	11: 32,160,875 (GRCm39)	C19*	probably null	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rnf150	G	A	8: 83,590,807 (GRCm39)	V57M	probably benign	Het
Rp9	A	G	9: 22,370,015 (GRCm39)	F51L	probably benign	Het
Sav1	A	T	12: 70,015,975 (GRCm39)	Y274*	probably null	Het
Scn4a	A	T	11: 106,236,503 (GRCm39)	D252E	probably damaging	Het
Scn5a	T	C	9: 119,379,724 (GRCm39)	T187A	probably damaging	Het
Sigirr	T	A	7: 140,672,333 (GRCm39)	D229V	probably benign	Het
Slc39a13	T	C	2: 90,896,031 (GRCm39)	S157G	possibly damaging	Het
Slc6a20a	A	G	9: 123,489,471 (GRCm39)	S191P	probably damaging	Het
Sorl1	C	A	9: 41,979,128 (GRCm39)	A457S	probably benign	Het
Spag5	A	G	11: 78,210,412 (GRCm39)		probably benign	Het
Spon1	A	G	7: 113,436,066 (GRCm39)	E119G	possibly damaging	Het
Spred2	T	A	11: 19,958,485 (GRCm39)		probably benign	Het
Sprr3	T	G	3: 92,364,784 (GRCm39)	Q20P	possibly damaging	Het
Strn3	A	T	12: 51,673,966 (GRCm39)	F464L	possibly damaging	Het
Sun1	A	G	5: 139,220,602 (GRCm39)		probably benign	Het
Sypl2	A	G	3: 108,133,486 (GRCm39)	W28R	possibly damaging	Het
Syt5	A	T	7: 4,545,813 (GRCm39)	V150D	probably damaging	Het
Tasor	T	C	14: 27,168,363 (GRCm39)	F302L	probably damaging	Het
Thsd7a	A	G	6: 12,379,604 (GRCm39)	I940T	possibly damaging	Het
Tlcd3b	C	T	7: 126,426,795 (GRCm39)	R73C	probably damaging	Het
Tnrc6a	T	A	7: 122,785,951 (GRCm39)		probably benign	Het
Trp53	T	A	11: 69,479,509 (GRCm39)	L203Q	probably damaging	Het
Tubgcp4	T	C	2: 121,005,900 (GRCm39)	V96A	probably benign	Het
Usp17la	A	G	7: 104,510,246 (GRCm39)	T284A	possibly damaging	Het
Usp34	T	C	11: 23,401,997 (GRCm39)	M2409T	probably benign	Het
Vmn2r100	C	A	17: 19,742,382 (GRCm39)	P252Q	possibly damaging	Het
Vmn2r56	A	G	7: 12,449,350 (GRCm39)	I296T	probably benign	Het
Vmn2r67	A	G	7: 84,799,900 (GRCm39)	V446A	probably damaging	Het
Zfp217	C	T	2: 169,957,382 (GRCm39)	A539T	probably benign	Het
Zfp267	T	C	3: 36,220,262 (GRCm39)	C762R	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
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'- TGACCAGCATCCTGCTTTTAATAGCTT -3'
(R):5'- GTGTAGCATTCACTTTCCTCACAGGT -3'

Sequencing Primer
(F):5'- CCTGCTTTTAATAGCTTACAGGG -3'
(R):5'- TCCTCACAGGTAAATCATCTGTAAG -3'

Posted On

2013-06-12