Incidental Mutation 'R9655:Kmt5a'
ID 735453
Institutional Source Beutler Lab
Gene Symbol Kmt5a
Ensembl Gene ENSMUSG00000049327
Gene Name lysine methyltransferase 5A
Synonyms 2410195B05Rik, PR-SET7, Setd8
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9655 (G1)
Quality Score 225.009
Status Not validated
Chromosome 5
Chromosomal Location 124577993-124600371 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 124589393 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 197 (Y197C)
Ref Sequence ENSEMBL: ENSMUSP00000098275 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000059580] [ENSMUST00000100709] [ENSMUST00000198451] [ENSMUST00000199798]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000059580
AA Change: Y183C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000052953
Gene: ENSMUSG00000049327
AA Change: Y183C

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 damaging
Transcript: ENSMUST00000100709
AA Change: Y197C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000098275
Gene: ENSMUSG00000049327
AA Change: Y197C

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 probably damaging
Transcript: ENSMUST00000198451
AA Change: Y128C

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000143207
Gene: ENSMUSG00000049327
AA Change: Y128C

DomainStartEndE-ValueType
Blast:SET 32 142 3e-45 BLAST
SET 159 286 9e-29 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000199798
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.8%
  • 10x: 99.4%
  • 20x: 98.7%
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: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933402N03Rik T A 7: 130,740,695 (GRCm39) I174F possibly damaging Het
Ada C A 2: 163,574,270 (GRCm39) V129F probably damaging Het
Adgrl4 G T 3: 151,248,450 (GRCm39) M707I probably damaging Het
Ahcyl A T 16: 45,974,564 (GRCm39) I271N probably damaging Het
Arrb2 A G 11: 70,331,073 (GRCm39) Q419R probably null Het
Atad2 A T 15: 57,998,303 (GRCm39) L23Q probably damaging Het
Btbd2 A T 10: 80,492,045 (GRCm39) F107Y probably benign Het
C7 T A 15: 5,041,464 (GRCm39) T481S probably damaging Het
Capn10 T A 1: 92,867,111 (GRCm39) W114R probably damaging Het
Ccdc121 C T 5: 31,644,976 (GRCm39) T243I probably benign Het
Cdc16 T A 8: 13,809,153 (GRCm39) D39E possibly damaging Het
Cfap74 A T 4: 155,522,665 (GRCm39) I684F Het
Cyp2c70 T A 19: 40,149,121 (GRCm39) N342Y possibly damaging Het
Dnah17 G A 11: 117,971,649 (GRCm39) T2128I possibly damaging Het
Dnah5 A G 15: 28,242,900 (GRCm39) N545S probably benign Het
Dnmt3c A G 2: 153,561,914 (GRCm39) N539S probably damaging Het
Elfn1 A G 5: 139,958,964 (GRCm39) E656G possibly damaging Het
Exd1 A T 2: 119,350,855 (GRCm39) C469S probably damaging Het
F5 A T 1: 164,021,730 (GRCm39) I1402F probably benign Het
Fam186a A G 15: 99,840,973 (GRCm39) L1757P probably damaging Het
Fbxo42 A T 4: 140,895,171 (GRCm39) R45W probably damaging Het
Fer1l5 T C 1: 36,460,696 (GRCm39) V1978A probably benign Het
Fpr1 T A 17: 18,097,618 (GRCm39) I124F probably damaging Het
Fry A T 5: 150,362,251 (GRCm39) D2173V possibly damaging Het
Gabbr2 G T 4: 46,815,684 (GRCm39) T228K possibly damaging Het
Galnt9 A T 5: 110,762,104 (GRCm39) Y414F probably damaging Het
Gask1a T A 9: 121,794,170 (GRCm39) L108Q probably benign Het
Ggt5 A T 10: 75,444,635 (GRCm39) M318L probably benign Het
Glod4 A C 11: 76,125,292 (GRCm39) S156A probably benign Het
Gm5431 A T 11: 48,785,799 (GRCm39) M192K probably benign Het
Golga5 C T 12: 102,446,008 (GRCm39) S421L possibly damaging Het
Gpr18 T C 14: 122,149,992 (GRCm39) D11G probably benign Het
Igf2bp3 C T 6: 49,064,338 (GRCm39) V560I probably benign Het
Igfals A G 17: 25,099,665 (GRCm39) N252S probably damaging Het
Ighv8-5 C T 12: 115,031,416 (GRCm39) C41Y probably damaging Het
Iqgap3 T A 3: 88,016,728 (GRCm39) V1070D possibly damaging Het
Kdr G A 5: 76,122,488 (GRCm39) A479V probably benign Het
Kidins220 T C 12: 25,047,295 (GRCm39) L247P probably damaging Het
Krt33a A C 11: 99,906,624 (GRCm39) probably null Het
Mageb3 A G 2: 121,785,649 (GRCm39) S18P unknown Het
Mast1 T A 8: 85,650,660 (GRCm39) Y387F probably damaging Het
Mcm5 C T 8: 75,844,168 (GRCm39) S313F probably benign Het
Med17 C T 9: 15,176,719 (GRCm39) V503M possibly damaging Het
Mpp3 A G 11: 101,899,481 (GRCm39) C347R probably benign Het
Mtr A G 13: 12,203,030 (GRCm39) L1191P probably damaging Het
Mybphl A T 3: 108,282,099 (GRCm39) I110F probably damaging Het
Nkx2-1 T A 12: 56,581,802 (GRCm39) D15V probably damaging Het
Nwd2 G A 5: 63,964,568 (GRCm39) W1384* probably null Het
Onecut1 A G 9: 74,770,330 (GRCm39) H251R possibly damaging Het
Or10ak8 T A 4: 118,773,804 (GRCm39) N287Y probably damaging Het
Or13f5 C T 4: 52,825,526 (GRCm39) T43I probably benign Het
Or51a6 A G 7: 102,604,319 (GRCm39) F163S probably damaging Het
Or8b37 A T 9: 37,959,387 (GRCm39) I290L probably benign Het
Palmd T C 3: 116,716,840 (GRCm39) *552W probably null Het
Pcdhgb2 A G 18: 37,823,285 (GRCm39) E92G probably damaging Het
Pcdhgb5 G T 18: 37,865,122 (GRCm39) E306* probably null Het
Peg10 CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG CCACATCAGGATCCACATCAGGATGCACATCAG 6: 4,756,398 (GRCm39) probably benign Het
Pex1 T A 5: 3,655,653 (GRCm39) L160Q probably damaging Het
Phxr2 A T 10: 98,961,974 (GRCm39) S29T unknown Het
Ppargc1a A G 5: 51,705,852 (GRCm39) probably null Het
Psmb11 T C 14: 54,862,965 (GRCm39) V61A probably damaging Het
Ripor2 A T 13: 24,908,983 (GRCm39) I1034F possibly damaging Het
Rnaset2b T A 17: 7,259,134 (GRCm39) N133K probably damaging Het
Rtn4 A G 11: 29,657,504 (GRCm39) T553A probably damaging Het
Samd9l T A 6: 3,373,578 (GRCm39) T1228S probably benign Het
Sdr42e2 A G 7: 120,430,279 (GRCm39) T379A probably benign Het
Shisal2a C A 4: 108,234,616 (GRCm39) V84L possibly damaging Het
Slc1a1 C T 19: 28,870,283 (GRCm39) A94V probably damaging Het
Snx31 C T 15: 36,534,582 (GRCm39) C197Y probably damaging Het
Tbc1d4 A G 14: 101,744,567 (GRCm39) V353A probably damaging Het
Tbc1d9b A G 11: 50,059,610 (GRCm39) D1004G possibly damaging Het
Tex15 T A 8: 34,066,784 (GRCm39) Y2071* probably null Het
Tnni3k G A 3: 154,645,410 (GRCm39) R492* probably null Het
Tns2 A G 15: 102,012,933 (GRCm39) H7R probably benign Het
Top2a G T 11: 98,905,334 (GRCm39) N369K probably damaging Het
Tpbg A T 9: 85,726,252 (GRCm39) T74S probably damaging Het
Trpm6 A G 19: 18,869,466 (GRCm39) N2018D probably benign Het
Trub2 A T 2: 29,669,833 (GRCm39) probably null Het
Vps13d A G 4: 144,813,305 (GRCm39) F3324L Het
Wdr20rt A T 12: 65,273,707 (GRCm39) Q390L probably benign Het
Wdr49 T A 3: 75,240,561 (GRCm39) D436V probably damaging Het
Zfp111 C T 7: 23,898,543 (GRCm39) G357D probably damaging Het
Zfp668 A G 7: 127,466,113 (GRCm39) V357A 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
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
Predicted Primers PCR Primer
(F):5'- GCCCAGGTAGATAAGCAGAC -3'
(R):5'- GATTGTTCTACGGCATCAAGTAC -3'

Sequencing Primer
(F):5'- GACATGCACCTAGGTCCCAG -3'
(R):5'- GTACCAGGGTCTTAAGAATGCCTC -3'
Posted On 2022-11-14