Incidental Mutation 'R0743:Kmt5a'
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Institutional Source Beutler Lab
Gene Symbol Kmt5a
Ensembl Gene ENSMUSG00000049327
Gene Namelysine methyltransferase 5A
SynonymsPR-SET7, Setd8, 2410195B05Rik
MMRRC Submission 038924-MU
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #R0743 (G1)
Quality Score225
Status Not validated
Chromosomal Location124439930-124462308 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) C to A at 124447219 bp
Amino Acid Change Asparagine to Lysine at position 44 (N44K)
Ref Sequence ENSEMBL: ENSMUSP00000052953 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000059580] [ENSMUST00000100709] [ENSMUST00000198451] [ENSMUST00000199798]
Predicted Effect probably damaging
Transcript: ENSMUST00000059580
AA Change: N44K

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000052953
Gene: ENSMUSG00000049327
AA Change: N44K

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: N58K

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000098275
Gene: ENSMUSG00000049327
AA Change: N58K

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
SMART Domains Protein: ENSMUSP00000143207
Gene: ENSMUSG00000049327

Blast:SET 32 142 3e-45 BLAST
SET 159 286 9e-29 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000199798
AA Change: R6S

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 96.7%
  • 20x: 92.7%
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc4 A T 14: 118,553,288 I844N possibly damaging Het
Bend7 A T 2: 4,744,244 K57N probably damaging Het
Cacna2d4 C T 6: 119,307,286 R745W probably damaging Het
Csmd2 A T 4: 128,113,676 T149S probably benign Het
Cyp2a12 T C 7: 27,032,542 I236T probably benign Het
Dnase1l2 A G 17: 24,441,880 V170A possibly damaging Het
Dnm2 T A 9: 21,500,265 Y597N probably damaging Het
Epsti1 A T 14: 77,931,275 R117S probably damaging Het
Gabarapl2 A T 8: 111,942,505 I32F probably damaging Het
Glrb T A 3: 80,879,680 I59F probably damaging Het
Gm13089 A T 4: 143,698,564 I103N probably damaging Het
Gm17689 T C 9: 36,581,301 S103G probably benign Het
Gosr1 A G 11: 76,730,146 I239T probably benign Het
Kif5b G T 18: 6,209,192 R857S probably damaging Het
Ksr1 A T 11: 79,021,503 H675Q possibly damaging Het
Maats1 A G 16: 38,335,634 F76L possibly damaging Het
Mep1b A G 18: 21,080,458 D68G possibly damaging Het
Nebl A C 2: 17,411,118 S327A probably benign Het
Nfat5 G A 8: 107,368,066 E962K probably damaging Het
Nfatc4 A C 14: 55,826,644 D126A probably damaging Het
Nmt2 A T 2: 3,314,785 R271* probably null Het
Nol7 G A 13: 43,400,615 V133I probably benign Het
Npepps A G 11: 97,206,058 probably benign Het
Nphp3 GCATCATCATCATCATC GCATCATCATCATC 9: 104,022,768 probably benign Het
Olfr1100 G A 2: 86,978,499 T99I probably benign Het
Olfr376 A T 11: 73,374,889 I47F probably benign Het
Olfr610 C T 7: 103,506,862 W28* probably null Het
Olfr798 T A 10: 129,625,843 T73S probably benign Het
Ovgp1 T A 3: 105,974,932 L37H probably damaging Het
Padi3 G T 4: 140,786,429 A646D probably benign Het
Pamr1 A G 2: 102,609,907 E142G probably damaging Het
Papolg A T 11: 23,870,818 probably null Het
Pfkl C T 10: 77,995,243 probably null Het
Plrg1 T C 3: 83,059,917 S132P probably benign Het
Prr14l C A 5: 32,831,194 C319F possibly damaging Het
Prtn3 T A 10: 79,879,677 M1K probably null Het
Ptpn22 T C 3: 103,902,171 F700S probably damaging Het
Ptprz1 C T 6: 23,044,367 Q1273* probably null Het
Rif1 GCCACCA GCCA 2: 52,110,324 probably benign Het
Ryr2 T C 13: 11,554,529 D4963G probably damaging Het
Sec16a G A 2: 26,419,722 L2091F possibly damaging Het
Senp6 C T 9: 80,093,589 R27C probably damaging Het
Shcbp1 T A 8: 4,764,906 M191L probably benign Het
Sirt4 T C 5: 115,482,955 K53E probably benign Het
Slc10a2 A G 8: 5,089,132 S271P probably damaging Het
Slc35b2 T A 17: 45,566,825 F293I probably damaging Het
Slc38a10 C T 11: 120,140,643 V103M probably damaging Het
St5 A G 7: 109,557,345 L66P probably damaging Het
Stab2 T A 10: 86,887,895 I1479F probably damaging Het
Synpo2 A G 3: 123,112,706 V987A probably benign Het
Syt9 A G 7: 107,436,561 I262V probably damaging Het
Taf2 GCTTCTTCTTCTTCTTCTT GCTTCTTCTTCTTCTT 15: 55,016,461 probably benign Het
Tmem39a A T 16: 38,585,402 I200F probably damaging Het
Ttn G A 2: 76,749,269 T23760M probably damaging Het
Uqcrc1 C T 9: 108,944,705 Q22* probably null Het
Wdtc1 A G 4: 133,300,661 W377R probably damaging Het
Zfp454 A G 11: 50,873,937 S223P probably benign Het
Other mutations in Kmt5a
AlleleSourceChrCoordTypePredicted EffectPPH 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
R1470:Kmt5a UTSW 5 124447271 missense probably damaging 0.97
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
Predicted Primers PCR Primer

Sequencing Primer
Posted On2013-09-30