Incidental Mutation 'R1470:Kmt5a'
ID 197935
Institutional Source Beutler Lab
Gene Symbol Kmt5a
Ensembl Gene ENSMUSG00000049327
Gene Name lysine methyltransferase 5A
Synonyms 2410195B05Rik, PR-SET7, Setd8
MMRRC Submission 039523-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1470 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 124577993-124600371 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 124585334 bp (GRCm39)
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] [ENSMUST00000199798] [ENSMUST00000198451]
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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 probably damaging
Transcript: ENSMUST00000199798
AA Change: L23P

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

DomainStartEndE-ValueType
Blast:SET 32 142 3e-45 BLAST
SET 159 286 9e-29 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147692
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154031
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147969
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143722
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 97.0%
  • 10x: 95.5%
  • 20x: 93.0%
Validation Efficiency 97% (125/129)
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: 142 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aak1 T A 6: 86,944,337 (GRCm39) S749T unknown Het
Abcb4 A T 5: 8,990,968 (GRCm39) I843F probably damaging Het
Abcb6 A T 1: 75,149,323 (GRCm39) probably benign Het
AC238840.1 A T 7: 38,467,377 (GRCm39) noncoding transcript Het
Actr8 T A 14: 29,708,926 (GRCm39) H244Q possibly damaging Het
Acyp2 A G 11: 30,456,452 (GRCm39) probably benign Het
Adgrv1 A G 13: 81,530,417 (GRCm39) Y5886H probably benign Het
Afap1 C T 5: 36,119,081 (GRCm39) probably benign Het
Agk T A 6: 40,363,751 (GRCm39) W244R probably damaging Het
Akirin1 T A 4: 123,631,883 (GRCm39) probably benign Het
Ankrd11 C A 8: 123,626,463 (GRCm39) V161L probably damaging Het
Arap3 T C 18: 38,122,249 (GRCm39) probably null Het
Arhgap29 A G 3: 121,785,968 (GRCm39) probably benign Het
Armc3 A G 2: 19,243,547 (GRCm39) M88V probably benign Het
Atp13a5 G T 16: 29,167,833 (GRCm39) P109T probably benign Het
Avpr1b T A 1: 131,528,323 (GRCm39) V282D probably damaging Het
Baz2b T C 2: 59,808,890 (GRCm39) K120E possibly damaging Het
Bltp1 T C 3: 37,052,480 (GRCm39) M3060T probably benign Het
Cacna1a T A 8: 85,241,579 (GRCm39) probably benign Het
Cacng6 G A 7: 3,473,404 (GRCm39) C76Y probably damaging Het
Cactin G T 10: 81,158,985 (GRCm39) E279* probably null Het
Car9 A G 4: 43,510,222 (GRCm39) Y268C probably damaging Het
Ccdc146 T A 5: 21,524,564 (GRCm39) I263F probably damaging Het
Cdc16 A T 8: 13,808,992 (GRCm39) probably benign Het
Cdh16 T G 8: 105,345,003 (GRCm39) S429R probably benign Het
Cep250 A G 2: 155,832,995 (GRCm39) E1639G probably damaging Het
Ces1d A T 8: 93,921,649 (GRCm39) V38D possibly damaging Het
Chd1 A T 17: 15,946,545 (GRCm39) Q97L possibly damaging Het
Ciita G A 16: 10,332,332 (GRCm39) D898N possibly damaging Het
Clstn1 A G 4: 149,719,179 (GRCm39) N336S possibly damaging Het
Cntnap5a A G 1: 116,187,249 (GRCm39) D607G probably damaging Het
Col1a2 G A 6: 4,518,822 (GRCm39) probably benign Het
Col20a1 C T 2: 180,636,753 (GRCm39) H245Y probably benign Het
Coq8b A T 7: 26,951,734 (GRCm39) T399S probably benign Het
Cpn2 A G 16: 30,079,003 (GRCm39) S233P probably benign Het
Cryz G A 3: 154,312,113 (GRCm39) G70D probably damaging Het
Csmd1 G T 8: 16,207,218 (GRCm39) probably benign Het
Def6 T A 17: 28,444,956 (GRCm39) D451E possibly damaging Het
Dnah8 T A 17: 30,966,251 (GRCm39) C2480* probably null Het
Dnah9 T C 11: 65,818,648 (GRCm39) N3230S probably benign Het
Dyrk4 G T 6: 126,893,337 (GRCm39) S15* probably null Het
Erc1 T C 6: 119,671,563 (GRCm39) R917G probably damaging Het
Fgd2 T A 17: 29,593,082 (GRCm39) probably benign Het
Frem3 G T 8: 81,337,820 (GRCm39) V38L probably benign Het
Gas2l3 T C 10: 89,249,796 (GRCm39) I441V probably benign Het
Gm14393 T A 2: 174,905,774 (GRCm39) Y6F probably damaging Het
Gm1527 A G 3: 28,969,417 (GRCm39) K256E possibly damaging Het
Gm21905 G T 5: 68,103,740 (GRCm39) probably benign Het
Gtf2ird1 T A 5: 134,424,656 (GRCm39) probably null Het
Hmces C A 6: 87,913,121 (GRCm39) T292K probably benign Het
Hpse2 G A 19: 43,376,692 (GRCm39) S20L probably benign Het
Ift70b G T 2: 75,768,155 (GRCm39) S199R probably benign Het
Ikbke A T 1: 131,204,224 (GRCm39) V23E probably null Het
Ino80 A T 2: 119,210,130 (GRCm39) V1387E probably damaging Het
Islr G T 9: 58,064,589 (GRCm39) A306D probably damaging Het
Jakmip1 G A 5: 37,258,182 (GRCm39) G276D probably damaging Het
Jchain A G 5: 88,673,979 (GRCm39) V55A probably benign Het
Kalrn T C 16: 34,007,841 (GRCm39) K1350E probably damaging Het
Kansl1l T C 1: 66,841,156 (GRCm39) Q48R possibly damaging Het
Lrba C T 3: 86,644,449 (GRCm39) H381Y probably damaging Het
Lrch3 T C 16: 32,808,865 (GRCm39) probably benign Het
Lrrc32 T C 7: 98,148,564 (GRCm39) V448A probably benign Het
Mapkbp1 T C 2: 119,848,301 (GRCm39) M617T probably damaging Het
Megf6 C T 4: 154,336,876 (GRCm39) probably benign Het
Mfap1a T C 2: 121,333,282 (GRCm39) M50V probably benign Het
Mgam G T 6: 40,736,062 (GRCm39) A854S probably damaging Het
Myh3 A C 11: 66,988,885 (GRCm39) probably benign Het
Myo18b C A 5: 112,840,899 (GRCm39) R2298L probably damaging Het
Myo1h T A 5: 114,457,765 (GRCm39) M92K probably damaging Het
Nfkbib T C 7: 28,461,447 (GRCm39) probably null Het
Nlrp2 T A 7: 5,303,950 (GRCm39) T192S probably benign Het
Nr2f1 A T 13: 78,346,284 (GRCm39) Y137N possibly damaging Het
Nup98 T A 7: 101,796,513 (GRCm39) D841V probably damaging Het
Nvl A G 1: 180,966,827 (GRCm39) V59A probably damaging Het
Ogdhl C A 14: 32,068,745 (GRCm39) N948K probably damaging Het
Or11g27 T C 14: 50,771,159 (GRCm39) S97P possibly damaging Het
Or12j3 A G 7: 139,953,026 (GRCm39) S166P probably benign Het
Or13a24 A G 7: 140,154,662 (GRCm39) T199A probably benign Het
Or51g1 A C 7: 102,633,530 (GRCm39) Y280* probably null Het
Orc2 A C 1: 58,520,317 (GRCm39) probably benign Het
Osgin1 G A 8: 120,171,704 (GRCm39) R166H probably damaging Het
Palb2 A T 7: 121,706,746 (GRCm39) F741I probably benign Het
Palb2 G T 7: 121,706,747 (GRCm39) Y740* probably null Het
Parvb G A 15: 84,155,453 (GRCm39) G46D probably damaging Het
Parvb G A 15: 84,155,509 (GRCm39) D65N probably benign Het
Pcsk2 A T 2: 143,388,438 (GRCm39) K10* probably null Het
Pde3a C T 6: 141,411,932 (GRCm39) A502V probably benign Het
Pfas T C 11: 68,882,185 (GRCm39) I893V probably benign Het
Pla2g4a A T 1: 149,716,471 (GRCm39) D663E probably damaging Het
Prickle2 G A 6: 92,435,583 (GRCm39) P6L probably damaging Het
Prx T A 7: 27,217,026 (GRCm39) M648K probably benign Het
Ptpn21 T C 12: 98,654,735 (GRCm39) N744S probably benign Het
Ptprq C T 10: 107,554,435 (GRCm39) V97M probably damaging Het
Pvr T C 7: 19,652,549 (GRCm39) E122G possibly damaging Het
Racgap1 T C 15: 99,537,656 (GRCm39) K15E probably damaging Het
Rock1 C T 18: 10,136,091 (GRCm39) probably null Het
Rorc T A 3: 94,304,609 (GRCm39) Y331* probably null Het
Rpl37 T C 15: 5,148,096 (GRCm39) V91A probably benign Het
Rrp36 T A 17: 46,983,306 (GRCm39) K103* probably null Het
Ryr3 T A 2: 112,483,352 (GRCm39) M4142L probably benign Het
Sash1 A T 10: 8,665,357 (GRCm39) L125H probably damaging Het
Scn5a T C 9: 119,365,541 (GRCm39) M369V possibly damaging Het
Siglec1 A T 2: 130,912,307 (GRCm39) N1678K probably benign Het
Slc15a5 A T 6: 138,049,992 (GRCm39) V141E probably benign Het
Slc43a1 T C 2: 84,690,020 (GRCm39) probably benign Het
Slc8a3 A T 12: 81,246,484 (GRCm39) H856Q probably benign Het
Spmip11 T C 15: 98,483,142 (GRCm39) probably benign Het
Sptlc2 T A 12: 87,402,414 (GRCm39) M171L probably benign Het
Srcap T A 7: 127,158,899 (GRCm39) probably benign Het
St6gal2 A G 17: 55,797,944 (GRCm39) D310G probably damaging Het
Susd2 T A 10: 75,473,888 (GRCm39) D689V probably damaging Het
Suz12 A T 11: 79,910,558 (GRCm39) E303V possibly damaging Het
Taldo1 C A 7: 140,978,500 (GRCm39) T150K probably damaging Het
Tex14 T C 11: 87,440,355 (GRCm39) probably benign Het
Tg T A 15: 66,721,312 (GRCm39) F274I possibly damaging Het
Tmem151b T C 17: 45,856,663 (GRCm39) D259G probably damaging Het
Tmem179 G T 12: 112,468,288 (GRCm39) H64Q probably benign Het
Tmem236 A G 2: 14,223,732 (GRCm39) T174A probably benign Het
Tmtc1 T A 6: 148,207,483 (GRCm39) probably benign Het
Tnc A T 4: 63,884,811 (GRCm39) N1821K probably damaging Het
Tnfrsf11a A G 1: 105,752,773 (GRCm39) N261S probably damaging Het
Traf6 G T 2: 101,526,994 (GRCm39) probably benign Het
Trank1 C A 9: 111,172,300 (GRCm39) F96L possibly damaging Het
Trim56 T A 5: 137,142,017 (GRCm39) I500F probably damaging Het
Ttll5 A G 12: 85,926,168 (GRCm39) I321V possibly damaging Het
Ttn C A 2: 76,608,367 (GRCm39) W17852L probably damaging Het
Twnk G A 19: 44,997,820 (GRCm39) V450M probably damaging Het
Uba52 A G 8: 70,962,206 (GRCm39) I127T possibly damaging Het
Ubr4 T A 4: 139,148,537 (GRCm39) probably null Het
Uggt1 A T 1: 36,215,877 (GRCm39) M130K probably benign Het
Ulk4 T A 9: 120,910,722 (GRCm39) T1101S probably benign Het
Urb1 A G 16: 90,548,902 (GRCm39) S2269P probably benign Het
Ush2a G T 1: 188,132,403 (GRCm39) R875L probably benign Het
Usp9y T A Y: 1,332,471 (GRCm39) H1624L probably benign Homo
Vipr1 T C 9: 121,494,586 (GRCm39) L308S possibly damaging Het
Vps50 G A 6: 3,517,777 (GRCm39) probably benign Het
Xdh T G 17: 74,198,107 (GRCm39) K1260T probably damaging Het
Yipf4 A G 17: 74,800,963 (GRCm39) I94V probably benign Het
Zfhx4 A G 3: 5,478,206 (GRCm39) *3582W probably null Het
Zfp58 T C 13: 67,640,144 (GRCm39) N116D possibly damaging Het
Zfp750 C A 11: 121,402,819 (GRCm39) R643L probably benign Het
Znfx1 A G 2: 166,884,507 (GRCm39) V51A possibly damaging Het
Other mutations in Kmt5a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01087:Kmt5a APN 5 124,589,443 (GRCm39) splice site probably benign
IGL01839:Kmt5a APN 5 124,589,417 (GRCm39) missense probably benign 0.08
R0540:Kmt5a UTSW 5 124,589,373 (GRCm39) missense probably damaging 1.00
R0743:Kmt5a UTSW 5 124,585,282 (GRCm39) missense probably damaging 1.00
R1470:Kmt5a UTSW 5 124,585,334 (GRCm39) missense probably damaging 0.97
R1496:Kmt5a UTSW 5 124,597,948 (GRCm39) frame shift probably null
R1676:Kmt5a UTSW 5 124,597,948 (GRCm39) frame shift probably null
R6596:Kmt5a UTSW 5 124,588,759 (GRCm39) missense probably benign 0.06
R7582:Kmt5a UTSW 5 124,597,982 (GRCm39) missense probably benign 0.04
R8534:Kmt5a UTSW 5 124,598,635 (GRCm39) missense probably benign 0.02
R8786:Kmt5a UTSW 5 124,584,074 (GRCm39) missense probably benign 0.00
R9201:Kmt5a UTSW 5 124,597,912 (GRCm39) missense probably damaging 1.00
R9377:Kmt5a UTSW 5 124,578,064 (GRCm39) start gained probably benign
R9655:Kmt5a UTSW 5 124,589,393 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGTATGTGTTCAGAAACCTGGGGC -3'
(R):5'- TCAATGTGGCAAGACACGACTGAAG -3'

Sequencing Primer
(F):5'- AGAATCTGCCGCAGCTCTC -3'
(R):5'- CGACTGAAGGATATGCTAACTCTTG -3'
Posted On 2014-05-23