Mutagenetix > Incidental Mutation

Incidental Mutation 'R7904:Kmt5c'

610158

Institutional Source

Beutler Lab

Gene Symbol

Kmt5c

Ensembl Gene

ENSMUSG00000059851

Gene Name

lysine methyltransferase 5C

Synonyms

Suv420h2, Suv4-20h2

MMRRC Submission

045956-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7904 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

4743114-4750513 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 4749158 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 264 (T264S)

Ref Sequence

ENSEMBL: ENSMUSP00000096452 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000098853] [ENSMUST00000108582] [ENSMUST00000108583] [ENSMUST00000128018] [ENSMUST00000130215] [ENSMUST00000160480]

AlphaFold

Q6Q783

PDB Structure

The structure of the Suv4-20h2 ternary complex with histone H4 [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000098853
AA Change: T264S

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000096452
Gene: ENSMUSG00000059851
AA Change: T264S

Domain	Start	End	E-Value	Type
Blast:SET	6	50	1e-10	BLAST
SET	110	224	1.17e-14	SMART
low complexity region	268	281	N/A	INTRINSIC
low complexity region	327	343	N/A	INTRINSIC
low complexity region	411	427	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000108582
AA Change: T264S

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000104223
Gene: ENSMUSG00000059851
AA Change: T264S

Domain	Start	End	E-Value	Type
Blast:SET	6	50	1e-10	BLAST
SET	110	224	1.17e-14	SMART
low complexity region	268	281	N/A	INTRINSIC
low complexity region	327	343	N/A	INTRINSIC
low complexity region	411	427	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000108583
AA Change: T264S

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000104224
Gene: ENSMUSG00000059851
AA Change: T264S

Domain	Start	End	E-Value	Type
Blast:SET	6	50	1e-10	BLAST
SET	110	224	1.17e-14	SMART
low complexity region	268	281	N/A	INTRINSIC
low complexity region	327	343	N/A	INTRINSIC
low complexity region	411	427	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000128018
AA Change: T72S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000114445
Gene: ENSMUSG00000059851
AA Change: T72S

Domain	Start	End	E-Value	Type
Blast:SET	1	32	4e-15	BLAST
PDB:4AU7\|B	1	54	5e-33	PDB
low complexity region	76	89	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000130215

SMART Domains

Protein: ENSMUSP00000119323
Gene: ENSMUSG00000059851

Domain	Start	End	E-Value	Type
PDB:4AU7\|B	1	164	1e-110	PDB
Blast:SET	32	133	5e-35	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000160480

SMART Domains

Protein: ENSMUSP00000124663
Gene: ENSMUSG00000059851

Domain	Start	End	E-Value	Type
PDB:4AU7\|B	1	36	2e-18	PDB
Blast:SET	6	36	3e-10	BLAST

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

97% (72/74)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] SUV420H2 and the related enzyme SUV420H1 (MIM 610881) function as histone methyltransferases that specifically trimethylate nucleosomal histone H4 (see MIM 602822) on lysine-20 (K20) (Schotta et al., 2004 [PubMed 15145825]).[supplied by OMIM, Dec 2009]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit no apparent defects and develop normally. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam8	G	A	7: 139,567,591 (GRCm39)	T384I	probably benign	Het
Astn1	T	C	1: 158,424,886 (GRCm39)	F691L	probably benign	Het
Azgp1	A	G	5: 137,985,869 (GRCm39)	E164G	probably damaging	Het
Bdp1	A	G	13: 100,177,944 (GRCm39)	V1975A	probably benign	Het
Cactin	T	C	10: 81,161,699 (GRCm39)	Y744H	possibly damaging	Het
Clstn1	T	A	4: 149,698,594 (GRCm39)	I60N	probably benign	Het
Col16a1	T	A	4: 129,948,001 (GRCm39)	C240*	probably null	Het
Col6a5	T	C	9: 105,805,720 (GRCm39)	D1062G	unknown	Het
Csmd2	T	C	4: 128,313,346 (GRCm39)	L1341P		Het
Cyp51	A	T	5: 4,150,173 (GRCm39)	F183L	probably damaging	Het
Dbnl	T	A	11: 5,741,779 (GRCm39)		probably null	Het
Ddx60	G	A	8: 62,430,924 (GRCm39)	V820I	possibly damaging	Het
Dnaaf9	A	T	2: 130,633,923 (GRCm39)		probably null	Het
Dnah11	T	A	12: 117,867,003 (GRCm39)	D4046V	possibly damaging	Het
Dnah6	G	A	6: 73,112,450 (GRCm39)		probably null	Het
Dnttip1	A	G	2: 164,589,472 (GRCm39)	Y89C	probably benign	Het
Efr3a	T	A	15: 65,696,527 (GRCm39)	V144E	probably damaging	Het
Epha8	T	C	4: 136,659,050 (GRCm39)	Q868R	possibly damaging	Het
Ercc5	G	T	1: 44,214,998 (GRCm39)		probably null	Het
Fam118a	A	G	15: 84,929,834 (GRCm39)	S21G	probably damaging	Het
Fam171b	T	C	2: 83,683,849 (GRCm39)	I122T	probably damaging	Het
Fat4	T	A	3: 38,941,690 (GRCm39)	S194R	probably damaging	Het
Fcho2	T	A	13: 98,932,871 (GRCm39)	T44S	possibly damaging	Het
Gm21698	C	A	5: 26,189,256 (GRCm39)	L232F	probably benign	Het
Gpr149	T	A	3: 62,502,356 (GRCm39)	D500V	probably benign	Het
Gpx8	T	A	13: 113,182,035 (GRCm39)	T133S	probably benign	Het
Hdlbp	A	T	1: 93,351,092 (GRCm39)	I542N	probably damaging	Het
Hid1	G	A	11: 115,246,187 (GRCm39)	S361F	probably damaging	Het
Igdcc4	C	A	9: 65,041,801 (GRCm39)	A1076E	probably benign	Het
Il4ra	A	G	7: 125,164,845 (GRCm39)	K7E	probably benign	Het
Inka2	T	C	3: 105,623,730 (GRCm39)	C35R	probably damaging	Het
Itga9	G	T	9: 118,706,294 (GRCm39)		probably null	Het
Kif5c	T	C	2: 49,591,095 (GRCm39)	S316P	probably damaging	Het
Litafd	A	G	16: 8,501,681 (GRCm39)	H61R		Het
Lrrc18	A	G	14: 32,731,052 (GRCm39)	N197S	probably benign	Het
Mcoln1	C	A	8: 3,558,356 (GRCm39)	D203E	probably benign	Het
Mitf	T	C	6: 97,990,671 (GRCm39)	V358A	probably damaging	Het
Mki67	A	T	7: 135,294,816 (GRCm39)	L3161Q	possibly damaging	Het
Mmp20	T	A	9: 7,644,076 (GRCm39)	F255I	possibly damaging	Het
Muc16	T	C	9: 18,566,946 (GRCm39)	T1858A	unknown	Het
Mug1	G	A	6: 121,828,424 (GRCm39)	V279I	probably benign	Het
Or6c68	T	C	10: 129,157,665 (GRCm39)	Y58H	probably damaging	Het
Otulin	G	T	15: 27,630,580 (GRCm39)	A39E	probably benign	Het
Pcdh17	A	T	14: 84,685,924 (GRCm39)	D797V	possibly damaging	Het
Pdlim5	G	A	3: 142,018,154 (GRCm39)	S147L	probably damaging	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm39)		probably benign	Het
Ppp2r1a	T	G	17: 21,182,003 (GRCm39)		probably null	Het
Ranbp6	T	C	19: 29,789,813 (GRCm39)	I180V	probably benign	Het
Rbm27	G	T	18: 42,465,921 (GRCm39)	R869L	probably damaging	Het
Rtn4r	A	G	16: 17,969,349 (GRCm39)	D259G	probably benign	Het
Ryr3	T	C	2: 112,611,369 (GRCm39)	E2271G	probably damaging	Het
Sbk1	A	G	7: 125,891,208 (GRCm39)	Y214C	probably damaging	Het
Scg3	C	T	9: 75,551,149 (GRCm39)	E459K	probably damaging	Het
Scin	T	G	12: 40,126,999 (GRCm39)	E449D	probably damaging	Het
Sel1l3	T	C	5: 53,297,166 (GRCm39)	K760R	probably benign	Het
Sh3pxd2a	A	G	19: 47,308,753 (GRCm39)	L145S	possibly damaging	Het
Sh3yl1	A	G	12: 30,991,995 (GRCm39)	D188G	probably benign	Het
Slc38a1	A	T	15: 96,521,921 (GRCm39)	L13Q	possibly damaging	Het
Smyd4	T	C	11: 75,240,613 (GRCm39)	I36T	possibly damaging	Het
Spata31f1a	A	G	4: 42,850,765 (GRCm39)	S464P	possibly damaging	Het
Stab2	A	T	10: 86,790,056 (GRCm39)	L570*	probably null	Het
Tg	G	T	15: 66,577,128 (GRCm39)	A1484S	probably benign	Het
Tm7sf2	A	T	19: 6,118,942 (GRCm39)	N677K	probably damaging	Het
Tmem235	T	G	11: 117,751,717 (GRCm39)	L47R	probably damaging	Het
Tmem87a	A	G	2: 120,210,198 (GRCm39)	S252P	probably damaging	Het
Unc13b	A	G	4: 43,217,075 (GRCm39)	D458G	probably benign	Het
Wfdc1	A	G	8: 120,406,770 (GRCm39)		probably null	Het
Wnt16	A	G	6: 22,297,989 (GRCm39)	Y285C	probably damaging	Het
Wwc2	A	T	8: 48,309,270 (GRCm39)	N837K	unknown	Het
Xdh	A	G	17: 74,229,467 (GRCm39)	F329L	probably benign	Het
Yaf2	G	T	15: 93,183,466 (GRCm39)	H115N	probably benign	Het
Zbtb16	G	T	9: 48,744,272 (GRCm39)	N13K	probably damaging	Het
Zfhx3	A	T	8: 109,677,695 (GRCm39)	D2915V	probably damaging	Het
Zfp236	A	T	18: 82,627,507 (GRCm39)	V1564E	possibly damaging	Het
Zfp407	G	T	18: 84,579,381 (GRCm39)	H577Q	not run	Het

Other mutations in Kmt5c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01340:Kmt5c	APN	7	4,745,140 (GRCm39)	nonsense	probably null
R0010:Kmt5c	UTSW	7	4,749,207 (GRCm39)	missense	probably benign	0.09
R0349:Kmt5c	UTSW	7	4,749,594 (GRCm39)	missense	probably damaging	0.98
R0400:Kmt5c	UTSW	7	4,749,243 (GRCm39)	missense	probably benign	0.02
R1402:Kmt5c	UTSW	7	4,745,252 (GRCm39)	missense	possibly damaging	0.62
R1402:Kmt5c	UTSW	7	4,745,252 (GRCm39)	missense	possibly damaging	0.62
R1599:Kmt5c	UTSW	7	4,744,899 (GRCm39)	missense	probably damaging	1.00
R1657:Kmt5c	UTSW	7	4,749,453 (GRCm39)	nonsense	probably null
R1799:Kmt5c	UTSW	7	4,745,729 (GRCm39)	critical splice donor site	probably null
R1892:Kmt5c	UTSW	7	4,745,714 (GRCm39)	nonsense	probably null
R3855:Kmt5c	UTSW	7	4,749,255 (GRCm39)	missense	probably damaging	1.00
R5982:Kmt5c	UTSW	7	4,749,790 (GRCm39)	missense	probably damaging	1.00
R6306:Kmt5c	UTSW	7	4,749,480 (GRCm39)	missense	probably benign	0.35
R6357:Kmt5c	UTSW	7	4,745,204 (GRCm39)	missense	possibly damaging	0.94
R6563:Kmt5c	UTSW	7	4,745,628 (GRCm39)	missense	probably damaging	1.00
R7106:Kmt5c	UTSW	7	4,745,705 (GRCm39)	missense	probably damaging	1.00
R8706:Kmt5c	UTSW	7	4,749,153 (GRCm39)	missense	probably damaging	1.00
R8777:Kmt5c	UTSW	7	4,745,712 (GRCm39)	missense	possibly damaging	0.93
R8777-TAIL:Kmt5c	UTSW	7	4,745,712 (GRCm39)	missense	possibly damaging	0.93
R9050:Kmt5c	UTSW	7	4,745,281 (GRCm39)	missense	probably benign	0.09
Z1177:Kmt5c	UTSW	7	4,749,699 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGTGAATGCTATACCTGTGAGAG -3'
(R):5'- TGTCAACAGGACCTGTGCAG -3'

Sequencing Primer
(F):5'- AGGTAGGCACGGACCTTGTG -3'
(R):5'- AACAGGACCTGTGCAGCTCTTC -3'

Posted On

2019-12-20