Mutagenetix > Incidental Mutation

Incidental Mutation 'R1470:Kmt5a'

165793

Institutional Source

Beutler Lab

Gene Symbol

Kmt5a

Ensembl Gene

ENSMUSG00000049327

Gene Name

lysine methyltransferase 5A

Synonyms

PR-SET7, Setd8, 2410195B05Rik

MMRRC Submission

039523-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1470 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

124439930-124462308 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 124447271 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 23 (L23P)

Ref Sequence

ENSEMBL: ENSMUSP00000143765 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000059580] [ENSMUST00000100709] [ENSMUST00000198451] [ENSMUST00000199798]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000059580
AA Change: S62P

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

SMART Domains

Protein: ENSMUSP00000052953
Gene: ENSMUSG00000049327
AA Change: S62P

Domain	Start	End	E-Value	Type
low complexity region	12	24	N/A	INTRINSIC
Blast:SET	87	197	2e-44	BLAST
SET	214	341	1.4e-26	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000100709
AA Change: S76P

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

SMART Domains

Protein: ENSMUSP00000098275
Gene: ENSMUSG00000049327
AA Change: S76P

Domain	Start	End	E-Value	Type
low complexity region	4	49	N/A	INTRINSIC
Blast:SET	101	211	1e-44	BLAST
SET	228	355	1.4e-26	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125588

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134826

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135667

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138766

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143722

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147692

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147969

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154031

Predicted Effect

probably benign
Transcript: ENSMUST00000198451
AA Change: S7P

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

SMART Domains

Protein: ENSMUSP00000143207
Gene: ENSMUSG00000049327
AA Change: S7P

Domain	Start	End	E-Value	Type
Blast:SET	32	142	3e-45	BLAST
SET	159	286	9e-29	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000199798
AA Change: L23P

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.7%
3x: 98.4%
10x: 90.6%
20x: 68.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a protein-lysine N-methyltransferase that can monomethylate Lys-20 of histone H4 to effect transcriptional repression of some genes. The encoded protein is required for cell proliferation and plays a role in chromatin condensation. [provided by RefSeq, May 2016]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit embryonic lethality. Mice homozygous for an allele lacking exon 7 die prior to implantation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 123 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932438A13Rik	T	C	3: 36,998,331	M3060T	probably benign	Het
Aak1	T	A	6: 86,967,355	S749T	unknown	Het
Abcb4	A	T	5: 8,940,968	I843F	probably damaging	Het
Actr8	T	A	14: 29,986,969	H244Q	possibly damaging	Het
Adgrv1	A	G	13: 81,382,298	Y5886H	probably benign	Het
Agk	T	A	6: 40,386,817	W244R	probably damaging	Het
Ankrd11	C	A	8: 122,899,724	V161L	probably damaging	Het
Arap3	T	C	18: 37,989,196		probably null	Het
Armc3	A	G	2: 19,238,736	M88V	probably benign	Het
Atp13a5	G	T	16: 29,349,015	P109T	probably benign	Het
Avpr1b	T	A	1: 131,600,585	V282D	probably damaging	Het
Baz2b	T	C	2: 59,978,546	K120E	possibly damaging	Het
Cacng6	G	A	7: 3,424,888	C76Y	probably damaging	Het
Cactin	G	T	10: 81,323,151	E279*	probably null	Het
Car9	A	G	4: 43,510,222	Y268C	probably damaging	Het
Ccdc146	T	A	5: 21,319,566	I263F	probably damaging	Het
Cdh16	T	G	8: 104,618,371	S429R	probably benign	Het
Cep250	A	G	2: 155,991,075	E1639G	probably damaging	Het
Ces1d	A	T	8: 93,195,021	V38D	possibly damaging	Het
Chd1	A	T	17: 15,726,283	Q97L	possibly damaging	Het
Ciita	G	A	16: 10,514,468	D898N	possibly damaging	Het
Clstn1	A	G	4: 149,634,722	N336S	possibly damaging	Het
Cntnap5a	A	G	1: 116,259,519	D607G	probably damaging	Het
Col1a2	G	A	6: 4,518,822		probably benign	Het
Col20a1	C	T	2: 180,994,960	H245Y	probably benign	Het
Coq8b	A	T	7: 27,252,309	T399S	probably benign	Het
Cpn2	A	G	16: 30,260,185	S233P	probably benign	Het
Cryz	G	A	3: 154,606,476	G70D	probably damaging	Het
Def6	T	A	17: 28,225,982	D451E	possibly damaging	Het
Dnah8	T	A	17: 30,747,277	C2480*	probably null	Het
Dnah9	T	C	11: 65,927,822	N3230S	probably benign	Het
Dyrk4	G	T	6: 126,916,374	S15*	probably null	Het
Erc1	T	C	6: 119,694,602	R917G	probably damaging	Het
Frem3	G	T	8: 80,611,191	V38L	probably benign	Het
Gas2l3	T	C	10: 89,413,934	I441V	probably benign	Het
Gm14393	T	A	2: 175,063,981	Y6F	probably damaging	Het
Gm1527	A	G	3: 28,915,268	K256E	possibly damaging	Het
Gm21905	G	T	5: 67,946,397		probably benign	Het
Gtf2ird1	T	A	5: 134,395,802		probably null	Het
Hmces	C	A	6: 87,936,139	T292K	probably benign	Het
Hpse2	G	A	19: 43,388,253	S20L	probably benign	Het
Ikbke	A	T	1: 131,276,487	V23E	probably null	Het
Ino80	A	T	2: 119,379,649	V1387E	probably damaging	Het
Islr	G	T	9: 58,157,306	A306D	probably damaging	Het
Jakmip1	G	A	5: 37,100,838	G276D	probably damaging	Het
Jchain	A	G	5: 88,526,120	V55A	probably benign	Het
Kalrn	T	C	16: 34,187,471	K1350E	probably damaging	Het
Kansl1l	T	C	1: 66,801,997	Q48R	possibly damaging	Het
Lrba	C	T	3: 86,737,142	H381Y	probably damaging	Het
Lrrc32	T	C	7: 98,499,357	V448A	probably benign	Het
Mapkbp1	T	C	2: 120,017,820	M617T	probably damaging	Het
Mfap1a	T	C	2: 121,502,801	M50V	probably benign	Het
Mgam	G	T	6: 40,759,128	A854S	probably damaging	Het
Myo18b	C	A	5: 112,693,033	R2298L	probably damaging	Het
Myo1h	T	A	5: 114,319,704	M92K	probably damaging	Het
Nlrp2	T	A	7: 5,300,951	T192S	probably benign	Het
Nr2f1	A	T	13: 78,198,165	Y137N	possibly damaging	Het
Nup98	T	A	7: 102,147,306	D841V	probably damaging	Het
Nvl	A	G	1: 181,139,262	V59A	probably damaging	Het
Ogdhl	C	A	14: 32,346,788	N948K	probably damaging	Het
Olfr530	A	G	7: 140,373,113	S166P	probably benign	Het
Olfr538	A	G	7: 140,574,749	T199A	probably benign	Het
Olfr578	A	C	7: 102,984,323	Y280*	probably null	Het
Olfr743	T	C	14: 50,533,702	S97P	possibly damaging	Het
Osgin1	G	A	8: 119,444,965	R166H	probably damaging	Het
Palb2	A	T	7: 122,107,523	F741I	probably benign	Het
Palb2	G	T	7: 122,107,524	Y740*	probably null	Het
Parvb	G	A	15: 84,271,308	D65N	probably benign	Het
Parvb	G	A	15: 84,271,252	G46D	probably damaging	Het
Pcsk2	A	T	2: 143,546,518	K10*	probably null	Het
Pde3a	C	T	6: 141,466,206	A502V	probably benign	Het
Pfas	T	C	11: 68,991,359	I893V	probably benign	Het
Pla2g4a	A	T	1: 149,840,720	D663E	probably damaging	Het
Prickle2	G	A	6: 92,458,602	P6L	probably damaging	Het
Prx	T	A	7: 27,517,601	M648K	probably benign	Het
Ptpn21	T	C	12: 98,688,476	N744S	probably benign	Het
Ptprq	C	T	10: 107,718,574	V97M	probably damaging	Het
Pvr	T	C	7: 19,918,624	E122G	possibly damaging	Het
Racgap1	T	C	15: 99,639,775	K15E	probably damaging	Het
Rock1	C	T	18: 10,136,091		probably null	Het
Rorc	T	A	3: 94,397,302	Y331*	probably null	Het
Rpl37	T	C	15: 5,118,614	V91A	probably benign	Het
Rrp36	T	A	17: 46,672,380	K103*	probably null	Het
Ryr3	T	A	2: 112,653,007	M4142L	probably benign	Het
Sash1	A	T	10: 8,789,593	L125H	probably damaging	Het
Scn5a	T	C	9: 119,536,475	M369V	possibly damaging	Het
Sfi1	TCGC	TC	11: 3,146,254		probably null	Het
Sfi1	C	CT	11: 3,146,255		probably null	Het
Siglec1	A	T	2: 131,070,387	N1678K	probably benign	Het
Slc15a5	A	T	6: 138,072,994	V141E	probably benign	Het
Slc8a3	A	T	12: 81,199,710	H856Q	probably benign	Het
Sptlc2	T	A	12: 87,355,640	M171L	probably benign	Het
Srcap	T	A	7: 127,559,727		probably benign	Het
St6gal2	A	G	17: 55,490,943	D310G	probably damaging	Het
Susd2	T	A	10: 75,638,054	D689V	probably damaging	Het
Suz12	A	T	11: 80,019,732	E303V	possibly damaging	Het
Taldo1	C	A	7: 141,398,587	T150K	probably damaging	Het
Tg	T	A	15: 66,849,463	F274I	possibly damaging	Het
Tmem151b	T	C	17: 45,545,737	D259G	probably damaging	Het
Tmem179	G	T	12: 112,501,854	H64Q	probably benign	Het
Tmem236	A	G	2: 14,218,921	T174A	probably benign	Het
Tnc	A	T	4: 63,966,574	N1821K	probably damaging	Het
Tnfrsf11a	A	G	1: 105,825,048	N261S	probably damaging	Het
Trank1	C	A	9: 111,343,232	F96L	possibly damaging	Het
Trim56	T	A	5: 137,113,163	I500F	probably damaging	Het
Ttc30b	G	T	2: 75,937,811	S199R	probably benign	Het
Ttll5	A	G	12: 85,879,394	I321V	possibly damaging	Het
Ttn	C	A	2: 76,778,023	W17852L	probably damaging	Het
Twnk	G	A	19: 45,009,381	V450M	probably damaging	Het
Uba52	A	G	8: 70,509,556	I127T	possibly damaging	Het
Ubr4	T	A	4: 139,421,226		probably null	Het
Uggt1	A	T	1: 36,176,796	M130K	probably benign	Het
Ulk4	T	A	9: 121,081,656	T1101S	probably benign	Het
Urb1	A	G	16: 90,752,014	S2269P	probably benign	Het
Ush2a	G	T	1: 188,400,206	R875L	probably benign	Het
Usp9y	T	A	Y: 1,332,471	H1624L	probably benign	Het
Vipr1	T	C	9: 121,665,520	L308S	possibly damaging	Het
Xdh	T	G	17: 73,891,112	K1260T	probably damaging	Het
Yipf4	A	G	17: 74,493,968	I94V	probably benign	Het
Zfhx4	A	G	3: 5,413,146	*3582W	probably null	Het
Zfp58	T	C	13: 67,492,025	N116D	possibly damaging	Het
Zfp750	C	A	11: 121,511,993	R643L	probably benign	Het
Znfx1	A	G	2: 167,042,587	V51A	possibly damaging	Het

Other mutations in Kmt5a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01087:Kmt5a	APN	5	124451380	splice site	probably benign
IGL01839:Kmt5a	APN	5	124451354	missense	probably benign	0.08
R0540:Kmt5a	UTSW	5	124451310	missense	probably damaging	1.00
R0743:Kmt5a	UTSW	5	124447219	missense	probably damaging	1.00
R1470:Kmt5a	UTSW	5	124447271	missense	probably damaging	0.97
R1496:Kmt5a	UTSW	5	124459885	frame shift	probably null
R1676:Kmt5a	UTSW	5	124459885	frame shift	probably null
R6596:Kmt5a	UTSW	5	124450696	missense	probably benign	0.06
R7582:Kmt5a	UTSW	5	124459919	missense	probably benign	0.04
R8534:Kmt5a	UTSW	5	124460572	missense	probably benign	0.02
R8786:Kmt5a	UTSW	5	124446011	missense	probably benign	0.00
R9201:Kmt5a	UTSW	5	124459849	missense	probably damaging	1.00
R9377:Kmt5a	UTSW	5	124440001	start gained	probably benign

Predicted Primers

PCR Primer
(F):5'- TGTATGTGTTCAGAAACCTGGGGC -3'
(R):5'- TCAATGTGGCAAGACACGACTGAAG -3'

Sequencing Primer
(F):5'- AGAATCTGCCGCAGCTCTC -3'
(R):5'- CGACTGAAGGATATGCTAACTCTTG -3'

Posted On

2014-03-28