Inspect variant sequences¶
The –print-protein and –print-protein-pretty options displays the full variant protein sequence in the variant_protein_seq field of the info when the genomic variant hits a protein-coding transcript.
Missense substitution¶
$ transvar ganno -i 'chr1:g.115256530G>A' --ensembl --print-protein
chr1:g.115256530G>A ENST00000369535 (protein_coding) NRAS -
chr1:g.115256530G>A/c.181C>T/p.Q61* inside_[cds_in_exon_3]
CSQN=Nonsense;variant_protein_seq=MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQ
VVIDGETCLLDILDTAG*;codon_pos=115256528-115256529-115256530;ref_codon_seq=CAA;
aliases=ENSP00000358548;source=Ensembl
–print-protein-pretty output is more human-readable and highlight the mutation in brackets.
$ transvar ganno --ccds -i 'chr3:g.178936091G>A' --print-protein-pretty
chr3:g.178936091G>A CCDS43171.1 (protein_coding) PIK3CA +
chr3:g.178936091G>A/c.1633G>A/p.E545K inside_[cds_in_exon_9]
CSQN=Missense;dbsnp=rs104886003(chr3:178936091G>A);variant_protein_seq=MPPRPS
SGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFF
DETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPH
SRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSE
QLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTA
TPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDI
YIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNK
ETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEIT_
_[E>K]__QEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGF
AVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESY
CRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEE
CRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCV
GLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIM
VKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFI
NLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIFHTIKQHALN*;codon_
pos=178936091-178936092-178936093;ref_codon_seq=GAG;source=CCDS
The alphabet transformation option –aa3 applies here as well.
$ transvar ganno -i 'chr1:g.115256530G>A' --ensembl --print-protein-pretty --aa3
chr1:g.115256530G>A ENST00000369535 (protein_coding) NRAS -
chr1:g.115256530G>A/c.181C>T/p.Gln61X inside_[cds_in_exon_3]
CSQN=Missense;variant_protein_seq=MetThrGluTyrLysLeuValValValGlyAlaGlyGlyValG
lyLysSerAlaLeuThrIleGlnLeuIleGlnAsnHisPheValAspGluTyrAspProThrIleGluAspSerTyr
ArgLysGlnValValIleAspGlyGluThrCysLeuLeuAspIleLeuAspThrAlaGly__[GluGluTyrSerAl
aMetArgAspGlnTyrMetArgThrGlyGluGlyPheLeuCysValPheAlaIleAsnAsnSerLysSerPheAlaA
spIleAsnLeuTyrArgGluGlnIleLysArgValLysAspSerAspAspValProMetValLeuValGlyAsnLys
CysAspLeuProThrArgThrValAspThrLysGlnAlaHisGluLeuAlaLysSerTyrGlyIleProPheIleGl
uThrSerAlaLysThrArgGlnGlyValGluAspAlaPheTyrThrLeuValArgGluIleArgGlnTyrArgMetL
ysLysLeuAsnSerSerAspAspGlyThrGlnGlyCysMetGlyLeuProCysValValMet>X];codon_pos=1
15256528-115256529-115256530;ref_codon_seq=CAA;aliases=ENSP00000358548;source
=Ensembl
Deletion¶
$ transvar canno --ccds -i 'CCDS8856:c.769_771delGGG' --print-protein-pretty
CCDS8856:c.769_771delGGG CCDS8856.1 (protein_coding) AAAS -
chr12:g.53703427_53703429delCCC/c.769_771delGGG/p.G257delG inside_[cds_in_exon_8]
CSQN=InFrameDeletion;left_align_gDNA=g.53703424_53703426delCCC;unaligned_gDNA
=g.53703424_53703426delCCC;left_align_cDNA=c.766_768delGGG;unalign_cDNA=c.769
_771delGGG;left_align_protein=p.G256delG;unalign_protein=p.G257delG;variant_p
rotein_seq=MCSLGLFPPPPPRGQVTLYEHNNELVTGSSYESPPPDFRGQWINLPVLQLTKDPLKTPGRLDHGTR
TAFIHHREQVWKRCINIWRDVGLFGVLNEIANSEEEVFEWVKTASGWALALCRWASSLHGSLFPHLSLRSEDLIAEF
AQVTNWSSCCLRVFAWHPHTNKFAVALLDDSVRVYNASSTIVPSLKHRLQRNVASLAWKPLSASVLAVACQSCILIW
TLDPTSLSTRPSSGCAQVLSHPGHTPVTSLAWAPSG__[G_deletion]__RLLSASPVDAAIRVWDVSTETCVPL
PWFRGGGVTNLLWSPDGSKILATTPSAVFRVWEAQMWTCERWPTLSGRCQTGCWSPDGSRLLFTVLGEPLIYSLSFP
ERCGEGKGCVGGAKSATIVADLSETTIQTPDGEERLGGEAHSMVWDPSGERLAVLMKGKPRVQDGKPVILLFRTRNS
PVFELLPCGIIQGEPGAQPQLITFHPSFNKGALLSVGWSTGRIAHIPLYFVNAQFPRFSPVLGRAQEPPAGGGGSIH
DLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL*;source=CCDS
Insertion¶
$ transvar ganno -i 'chr2:g.69741762_69741763insTGC' --ccds --print-protein-pretty
chr2:g.69741762_69741763insTGC CCDS1893.2 (protein_coding) AAK1 -
chr2:g.69741780_69741782dupCTG/c.1614_1616dupGCA/p.Q546dupQ inside_[cds_in_exon_12]
CSQN=InFrameInsertion;left_align_gDNA=g.69741762_69741763insTGC;unalign_gDNA=
g.69741762_69741763insTGC;left_align_cDNA=c.1596_1597insCAG;unalign_cDNA=c.16
14_1616dupGCA;left_align_protein=p.Y532_Q533insQ;unalign_protein=p.Q539dupQ;v
ariant_protein_seq=MKKFFDSRREQGGSGLGSGSSGGGGSTSGLGSGYIGRVFGIGRQQVTVDEVLAEGGFA
IVFLVRTSNGMKCALKRMFVNNEHDLQVCKREIQIMRDLSGHKNIVGYIDSSINNVSSGDVWEVLILMDFCRGGQVV
NLMNQRLQTGFTENEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLHDRGHYVLCDFGSATNKFQNPQTEGVNA
VEDEIKKYTTLSYRAPEMVNLYSGKIITTKADIWALGCLLYKLCYFTLPFGESQVAICDGNFTIPDNSRYSQDMHCL
IRYMLEPDPDKRPDIYQVSYFSFKLLKKECPIPNVQNSPIPAKLPEPVKASEAAAKKTQPKARLTDPIPTTETSIAP
RQRPKAGQTQPNPGILPIQPALTPRKRATVQPPPQAAGSSNQPGLLASVPQPKPQAPPSQPLPQTQAKQPQAPPTPQ
QTPSTQAQGLPAQAQATPQHQQQLFLKQQQQQQQPPPAQQQPAGTFYQQQQAQTQQFQAVHPATQKPAIAQFPVVSQ
GGSQQQLMQNFYQQQQQQQQQQQQQQ__[insert_Q]__LATALHQQQLMTQQAALQQKPTMAAGQQPQPQPAAAP
QPAPAQEPAIQAPVRQQPKVQTTPPPAVQGQKVGSLTPPSSPKTQRAGHRRILSDVTHSAVFGVPASKSTQLLQAAA
AEASLNKSKSATTTPSGSPRTSQQNVYNPSEGSTWNPFDDDNFSKLTAEELLNKDFAKLGEGKHPEKLGGSAESLIP
GFQSTQGDAFATTSFSAGTAEKRKGGQTVDSGLPLLSVSDPFIPLQVPDAPEKLIEGLKSPDTSLLLPDLLPMTDPF
GSTSDAVIEKADVAVESLIPGLEPPVPQRLPSQTESVTSNRTDSLTGEDSLLDCSLLSNPTTDLLEEFAPTAISAPV
HKAAEDSNLISGFDVPEGSDKVAEDEFDPIPVLITKNPQGGHSRNSSGSSESSLPNLARSLLLVDQLIDL*;phase
=2;source=CCDS
Block substitution¶
$ transvar ganno -i "chr2:g.234183372_234183383del" --ccds --print-protein-pretty
chr2:g.234183372_234183383del CCDS2502.2 (protein_coding) ATG16L1 +
chr2:g.234183372_234183383del12/c.845_856del12/p.H282_G286delinsR inside_[cds_in_exon_8]
CSQN=MultiAAMissense;left_align_gDNA=g.234183372_234183383del12;unaligned_gDN
A=g.234183372_234183383del12;left_align_cDNA=c.845_856del12;unalign_cDNA=c.84
5_856del12;variant_protein_seq=MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKS
DLHSVLAQKLQAEKHDVPNRHEISPGHDGTWNDNQLQEMAQLRIKHQEELTELHKKRGELAQLVIDLNNQMQRKDRE
MQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKLRKTTEENQELVTRWMAEKAQ
EANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATRRSVSSFPVPQD
NVDT__[HPGSG>R]__KEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGEKCEFKGSLSGS
NAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLKLWDLRSKVC
IKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSRDDLLKVIDLRT
NAIKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLYIWSVLTGKVEKVLSKQHSSSINAVAWSPSGSHVVSVD
KGCKAVLWAQY*;source=CCDS
chr2:g.234183372_234183383del CCDS2503.2 (protein_coding) ATG16L1 +
chr2:g.234183372_234183383del12/c.902_913del12/p.H301_G305delinsR inside_[cds_in_exon_9]
CSQN=MultiAAMissense;left_align_gDNA=g.234183372_234183383del12;unaligned_gDN
A=g.234183372_234183383del12;left_align_cDNA=c.902_913del12;unalign_cDNA=c.90
2_913del12;variant_protein_seq=MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKS
DLHSVLAQKLQAEKHDVPNRHEISPGHDGTWNDNQLQEMAQLRIKHQEELTELHKKRGELAQLVIDLNNQMQRKDRE
MQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKLRKTTEENQELVTRWMAEKAQ
EANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATKRLSQPAGGLLD
SITNIFGRRSVSSFPVPQDNVDT__[HPGSG>R]__KEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRV
KLWEVFGEKCEFKGSLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARI
VSGSHDRTLKLWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPER
TELLSCSRDDLLKVIDLRTNAIKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLYIWSVLTGKVEKVLSKQHS
SSINAVAWSPSGSHVVSVDKGCKAVLWAQY*;source=CCDS
chr2:g.234183372_234183383del CCDS54438.1 (protein_coding) ATG16L1 +
chr2:g.234183372_234183383del12/c.413_424del12/p.H138_G142delinsR inside_[cds_in_exon_5]
CSQN=MultiAAMissense;left_align_gDNA=g.234183372_234183383del12;unaligned_gDN
A=g.234183372_234183383del12;left_align_cDNA=c.413_424del12;unalign_cDNA=c.41
3_424del12;variant_protein_seq=MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKS
DLHSVLAQKLQAEKHDVPNRHEIRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATRR
SVSSFPVPQDNVDT__[HPGSG>R]__KEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGEK
CEFKGSLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTL
KLWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSRD
DLLKVIDLRTNAIKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLYIWSVLTGKVEKVLSKQHSSSINAVAWS
PSGSHVVSVDKGCKAVLWAQY*;source=CCDS
Frameshift sequence¶
$ transvar canno --ccds -i 'CCDS8856:c.769_770delGG' --print-protein-pretty
CCDS8856:c.769_770delGG CCDS8856.1 (protein_coding) AAAS -
chr12:g.53703428_53703429delCC/c.770_771delGG/p.G257Afs*65 inside_[cds_in_exon_8]
CSQN=Frameshift;left_align_gDNA=g.53703424_53703425delCC;unaligned_gDNA=g.537
03425_53703426delCC;left_align_cDNA=c.766_767delGG;unalign_cDNA=c.769_770delG
G;variant_protein_seq=MCSLGLFPPPPPRGQVTLYEHNNELVTGSSYESPPPDFRGQWINLPVLQLTKDPL
KTPGRLDHGTRTAFIHHREQVWKRCINIWRDVGLFGVLNEIANSEEEVFEWVKTASGWALALCRWASSLHGSLFPHL
SLRSEDLIAEFAQVTNWSSCCLRVFAWHPHTNKFAVALLDDSVRVYNASSTIVPSLKHRLQRNVASLAWKPLSASVL
AVACQSCILIWTLDPTSLSTRPSSGCAQVLSHPGHTPVTSLAWAPSG__[frameshift_GRLLSASPVDAAIRVW
DVSTETCVPLPWFRGGGVTNLLWSPDGSKILATTPSAVFRVWEAQMWTCERWPTLSGRCQTGCWSPDGSRLLFTVLG
EPLIYSLSFPERCGEGKGCVGGAKSATIVADLSETTIQTPDGEERLGGEAHSMVWDPSGERLAVLMKGKPRVQDGKP
VILLFRTRNSPVFELLPCGIIQGEPGAQPQLITFHPSFNKGALLSVGWSTGRIAHIPLYFVNAQFPRFSPVLGRAQE
PPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL*>AAALSFTRGCCYPGMGCLNRDLCPPSLVPRRW
GDQPALVPRRQQNPGYHSFSCLSSLGGPDVDL*];source=CCDS
$ transvar canno -i 'CCDS54438:c.409_421del' --ccds --print-protein-pretty
CCDS54438:c.409_421del CCDS54438.1 (protein_coding) ATG16L1 +
chr2:g.234183368_234183380del13/c.409_421del13/p.T137Lfs*5 inside_[cds_in_exon_5]
CSQN=Frameshift;left_align_gDNA=g.234183367_234183379del13;unaligned_gDNA=g.2
34183368_234183380del13;left_align_cDNA=c.408_420del13;unalign_cDNA=c.409_421
del13;variant_protein_seq=MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSV
LAQKLQAEKHDVPNRHEIRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATRRSVSSF
PVPQDNVD__[frameshift_THPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGE
KCEFKGSLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRT
LKLWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSR
DDLLKVIDLRTNAIKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLYIWSVLTGKVEKVLSKQHSSSINAVAW
SPSGSHVVSVDKGCKAVLWAQY*>LVKK*];source=CCDS