How to identify first codon (Methionine) misssense variants?

Hugo_Symbol Variant_Classification  tx  exon    txChange    aaChange    Variant_Type    sample_id   Func.refGene    Gene.refGene    GeneDetail.refGene  ExonicFunc.refGene  AAChange.refGene    Func.knownGene  Gene.knownGene  GeneDetail.knownGene    ExonicFunc.knownGene    AAChange.knownGene  Func.ensGene    Gene.ensGene    GeneDetail.ensGene  ExonicFunc.ensGene  AAChange.ensGene
PRKCZ   Missense_Mutation   NM_002744   exon1   c.G50T  p.R17L  SNP 1901797K_anno   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon1:c.G50T:p.R17L exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon1:c.G50T:p.R17L    exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000378567:exon1:c.G50T:p.R17L,ENSG00000067606:ENST00000468310:exon1:c.G50T:p.R17L
PRKCZ   Missense_Mutation   NM_002744   exon2   c.G97T  p.A33S  SNP 1902400K_anno   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon2:c.G97T:p.A33S exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon2:c.G97T:p.A33S    exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000378567:exon2:c.G97T:p.A33S,ENSG00000067606:ENST00000468310:exon2:c.G97T:p.A33S
PRKCZ   Missense_Mutation   NM_002744   exon2   c.C98A  p.A33D  SNP B2001120K_anno  exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon2:c.C98A:p.A33D exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon2:c.C98A:p.A33D    exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000378567:exon2:c.C98A:p.A33D,ENSG00000067606:ENST00000468310:exon2:c.C98A:p.A33D
PRKCZ   Missense_Mutation   NM_002744   exon2   c.C164A p.P55Q  SNP 1800772K_anno   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon2:c.C164A:p.P55Q    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon2:c.C164A:p.P55Q   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000378567:exon2:c.C164A:p.P55Q,ENSG00000067606:ENST00000468310:exon2:c.C164A:p.P55Q,ENSG00000067606:ENST00000503297:exon2:c.C26A:p.P9Q
PRKCZ   Missense_Mutation   NM_002744   exon2   c.C172A p.L58I  SNP 1800772K_anno   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon2:c.C172A:p.L58I    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon2:c.C172A:p.L58I   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000378567:exon2:c.C172A:p.L58I,ENSG00000067606:ENST00000468310:exon2:c.C172A:p.L58I,ENSG00000067606:ENST00000503297:exon2:c.C34A:p.L12I
PRKCZ   Missense_Mutation   NM_002744   exon2   c.C172A p.L58I  SNP 1800782K_anno   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon2:c.C172A:p.L58I    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon2:c.C172A:p.L58I   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000378567:exon2:c.C172A:p.L58I,ENSG00000067606:ENST00000468310:exon2:c.C172A:p.L58I,ENSG00000067606:ENST00000503297:exon2:c.C34A:p.L12I
PRKCZ   Missense_Mutation   NM_002744   exon2   c.C172A p.L58I  SNP 1800816K_anno   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon2:c.C172A:p.L58I    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon2:c.C172A:p.L58I   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000378567:exon2:c.C172A:p.L58I,ENSG00000067606:ENST00000468310:exon2:c.C172A:p.L58I,ENSG00000067606:ENST00000503297:exon2:c.C34A:p.L12I
PRKCZ   Missense_Mutation   NM_002744   exon3   c.C217A p.Q73K  SNP 1800853K_anno   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon3:c.C217A:p.Q73K    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon3:c.C217A:p.Q73K   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000378567:exon3:c.C217A:p.Q73K,ENSG00000067606:ENST00000503297:exon3:c.C79A:p.Q27K
PRKCZ   Missense_Mutation   NM_002744   exon3   c.G260T p.R87M  SNP 1801038K_anno   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon3:c.G260T:p.R87M    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon3:c.G260T:p.R87M   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000378567:exon3:c.G260T:p.R87M,ENSG00000067606:ENST00000503297:exon3:c.G122T:p.R41M
PRKCZ   Missense_Mutation   NM_002744   exon4   c.C290A p.P97Q  SNP 1800791K_anno   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon4:c.C290A:p.P97Q    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon4:c.C290A:p.P97Q   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000468310:exon3:c.C200A:p.P67Q,ENSG00000067606:ENST00000378567:exon4:c.C290A:p.P97Q,ENSG00000067606:ENST00000503297:exon4:c.C152A:p.P51Q
PRKCZ   Missense_Mutation   NM_002744   exon4   c.C290A p.P97Q  SNP B2000359K_anno  exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon4:c.C290A:p.P97Q    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon4:c.C290A:p.P97Q   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000468310:exon3:c.C200A:p.P67Q,ENSG00000067606:ENST00000378567:exon4:c.C290A:p.P97Q,ENSG00000067606:ENST00000503297:exon4:c.C152A:p.P51Q
PRKCZ   Missense_Mutation   NM_002744   exon4   c.C290A p.P97Q  SNP B2000415K_anno  exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon4:c.C290A:p.P97Q    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon4:c.C290A:p.P97Q   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000468310:exon3:c.C200A:p.P67Q,ENSG00000067606:ENST00000378567:exon4:c.C290A:p.P97Q,ENSG00000067606:ENST00000503297:exon4:c.C152A:p.P51Q
PRKCZ   Missense_Mutation   NM_002744   exon4   c.C290A p.P97Q  SNP B2001619K_anno  exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon4:c.C290A:p.P97Q    exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon4:c.C290A:p.P97Q   exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000468310:exon3:c.C200A:p.P67Q,ENSG00000067606:ENST00000378567:exon4:c.C290A:p.P97Q,ENSG00000067606:ENST00000503297:exon4:c.C152A:p.P51Q
PRKCZ   Missense_Mutation   NM_002744   exon4   c.C298A p.P100T SNP B2001256K_anno  exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:NM_002744:exon4:c.C298A:p.P100T   exonic  PRKCZ   .   nonsynonymous SNV   PRKCZ:uc001aiq.3:exon4:c.C298A:p.P100T  exonic  ENSG00000067606 .   nonsynonymous SNV   ENSG00000067606:ENST00000468310:exon3:c.C208A:p.P70T,ENSG00000067606:ENST00000378567:exon4:c.C298A:p.P100T,ENSG00000067606:ENST00000503297:exon4:c.C160A:p.P54T
Here is an example of annotation file of missense variant. I want to know how to identify the first codon missense variants. Any help is appreciated.
mutation annovar missense
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updated 5.3 years ago by Pierre Lindenbaum
• written 5.3 years ago by lincaijin1994 •
lines where aaChange matches 'p.M1[A-Z]*'
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written 5.3 years ago by Pierre Lindenbaum
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