Protein level annotation¶
Protein level inputs are handled by the panno subcommand.
Protein sites¶
To use uniprot id as protein name, one must first download the uniprot id map by
transvar config --download_idmap
Then one could use protein id instead of gene name by applying the –idmap uniprot option to TransVar. For example,
$ transvar panno --ccds -i 'Q5VUM1:47' --idmap uniprot
Q5VUM1:47 CCDS4972.1 (protein_coding) C6ORF57 +
chr6:g.71289191_71289193/c.139_141/p.47S inside_[cds_in_exon_2]
protein_sequence=S;cDNA_sequence=TCC;gDNA_sequence=TCC;source=CCDS
TransVar use a keyword extension ref in Q5VUM1:p.47refS to differentiate from the synonymous mutation Q5VUM1:p.47S. The former notation specifies that the reference protein sequence is S while the later specifies the target protein sequence is S.
Protein motif¶
For example, one can find the genomic location of a DRY motif in protein P28222 by issuing the following command,
$ transvar panno -i 'P28222:p.146_148refDRY' --ccds --idmap uniprot
P28222:p.146_148refDRY CCDS4986.1 (protein_coding) HTR1B -
chr6:g.78172677_78172685/c.436_444/p.D146_Y148 inside_[cds_in_exon_1]
protein_sequence=DRY;cDNA_sequence=GACCGCTAC;gDNA_sequence=GTAGCGGTC;source=C
CDS
One can also use wildcard x (lowercase) in the motif.
$ transvar panno -i 'HTR1B:p.365_369refNPxxY' --ccds --seqmax 30
HTR1B:p.365_369refNPxxY CCDS4986.1 (protein_coding) HTR1B -
chr6:g.78172014_78172028/c.1093_1107/p.N365_Y369 inside_[cds_in_exon_1]
protein_sequence=NPIIY;cDNA_sequence=AACCCCATAATCTAT;gDNA_sequence=ATAGATTATG
GGGTT;source=CCDS
Protein region¶
$ transvar panno --ccds -i 'ABCB11:p.200_400'
outputs
ABCB11:p.200_400 CCDS46444.1 (protein_coding) ABCB11 -
chr2:g.169833195_169851872/c.598_1200/p.T200_K400 inside_[cds_in_exons_[6,7,8,9,10,11]]
protein_sequence=TRF..DRK;cDNA_sequence=ACA..AAA;gDNA_sequence=TTT..TGT;sourc
e=CCDS
Protein variants¶
Single amino acid substitution¶
Mutation formats acceptable in TransVar are `PIK3CA:p.E545K` or without reference or alternative amino acid identity, e.g., `PIK3CA:p.545K` or `PIK3CA:p.E545`. TransVar takes native HGVS format inputs and outputs. The reference amino acid is used to narrow the search scope of candidate transcripts. The alternative amino acid is used to infer nucleotide change which results in the amino acid.
$ transvar panno -i PIK3CA:p.E545K --ensembl
outputs
PIK3CA:p.E545K ENST00000263967 (protein_coding) PIK3CA +
chr3:g.178936091G>A/c.1633G>A/p.E545K inside_[cds_in_exon_10]
CSQN=Missense;reference_codon=GAG;candidate_codons=AAG,AAA;candidate_mnv_vari
ants=chr3:g.178936091_178936093delGAGinsAAA;dbsnp=rs104886003(chr3:178936091G
>A);aliases=ENSP00000263967;source=Ensembl
One may encounter ambiguous cases where the multiple substitutions exist in explaining the amino acid change. For example,
$ transvar panno -i ACSL4:p.R133R --ccds
outputs
ACSL4:p.R133R CCDS14548.1 (protein_coding) ACSL4 -
chrX:g.108926078G>T/c.399C>A/p.R133R inside_[cds_in_exon_2]
CSQN=Synonymous;reference_codon=CGC;candidate_codons=AGG,AGA,CGA,CGG,CGT;cand
idate_snv_variants=chrX:g.108926078G>C,chrX:g.108926078G>A;candidate_mnv_vari
ants=chrX:g.108926078_108926080delGCGinsCCT,chrX:g.108926078_108926080delGCGi
nsTCT;source=CCDS
In those cases, TransVar prioritizes all the candidate base changes by minimizing the edit distance between the reference codon sequence and the target codon sequence. One of the optimal base changes is arbitrarily chosen as the default and all the candidates are included in the appended CddMuts entry.
Ambiguous amino acid code¶
TransVar instantiates input of ambiguous amino acid code such as (‘B’, for “Asx”, which stands for “Asp” or “Asn”) to more specific amino acid. Even if the reference amino acid is a subset of the ambiguous alternative amino acid, TransVar assume a mutation on the nucleotide level (can still deduce synonymous mutations):
$ transvar panno -i 'APC:p.D326B' --ccds
APC:p.D326B CCDS4107.1 (protein_coding) APC +
chr5:g.112154705G>A/c.976G>A/p.D326N inside_[cds_in_exon_9]
CSQN=Missense;reference_codon=GAT;candidate_codons=AAC,AAT,GAC;candidate_snv_
variants=chr5:g.112154707T>C;candidate_mnv_variants=chr5:g.112154705_11215470
7delGATinsAAC;source=CCDS
Here input alternative amino acids is B (D or N). After TransVar processing, a ‘N’ is derived (though a D is equally likely, as shown in the candidates).
Insertion¶
$ transvar panno --ccds -i 'AATK:p.P1331_A1332insTP'
AATK:p.P1331_A1332insTP CCDS45807.1 (protein_coding) AATK -
chr17:g.79093270_79093271insAGGTGT/c.3993_3994insACACCT/p.T1330_P1331dupTP inside_[cds_in_exon_13]
CSQN=InFrameInsertion;left_align_protein=p.A1326_P1327insPT;unalign_protein=p
.T1330_P1331dupTP;left_align_gDNA=g.79093270_79093271insAGGTGT;unalign_gDNA=g
.79093270_79093271insAGGTGT;left_align_cDNA=c.3993_3994insACACCT;unalign_cDNA
=c.3993_3994insACACCT;16_CandidatesOmitted;source=CCDS
Deletion¶
$ transvar panno --ccds -i 'AADACL4:p.W263_I267delWRDAI'
AADACL4:p.W263_I267delWRDAI CCDS30590.1 (protein_coding) AADACL4 +
chr1:g.12726310_12726324del15/c.788_802del15/p.W263_I267delWRDAI inside_[cds_in_exon_4]
CSQN=InFrameDeletion;left_align_gDNA=g.12726308_12726322del15;unaligned_gDNA=
g.12726309_12726323del15;left_align_cDNA=c.786_800del15;unalign_cDNA=c.787_80
1del15;left_align_protein=p.W263_I267delWRDAI;unalign_protein=p.W263_I267delW
RDAI;imprecise;source=CCDS
Block substitution¶
$ transvar panno --ccds -i 'ABCC3:p.Y556_V557delinsRRR'
ABCC3:p.Y556_V557delinsRRR CCDS32681.1 (protein_coding) ABCC3 +
chr17:g.48745254_48745259delinsAGGAGGAGG/c.1666_1671delinsAGGAGGAGG/p.Y556_V557delinsRRR inside_[cds_in_exon_13]
CSQN=MultiAAMissense;216_CandidatesOmitted;source=CCDS
Sometimes block substitution comes from in-frame deletion on the nucleotide level.
$ transvar panno -i 'MAP2K1:p.F53_Q58delinsL' --ensembl
MAP2K1:p.F53_Q58delinsL ENST00000307102 (protein_coding) MAP2K1 +
chr15:g.66727443_66727457del15/c.159_173del15/p.F53_Q58delinsL inside_[cds_in_exon_2]
CSQN=MultiAAMissense;left_align_gDNA=g.66727443_66727457del15;unaligned_gDNA=
g.66727443_66727457del15;left_align_cDNA=c.159_173del15;unalign_cDNA=c.159_17
3del15;candidate_alternative_sequence=CTT/CTG/CTA/CTC/TTA/TTG;aliases=ENSP000
00302486;source=Ensembl
Frame-shift variants¶
Frame-shift variants can be results of either insertion or deletion. In the cases where both are plausible the variants are prioritized by the length of the insertion/deletion. Mutations of smallest variants are given as the most likely inference. Other candidates are in given in the candidates field.
$ transvar panno --refseq -i 'PTEN:p.T319fs*1' --max-candidates 2
PTEN:p.T319fs*1 NM_000314.4 (protein_coding) PTEN +
chr10:g.89720803_89720804insTA/c.954_955insTA/p.T319fs*1 inside_[cds_in_exon_8]
CSQN=Frameshift;left_align_cDNA=c.954_955insTA;left_align_gDNA=g.89720803_897
20804insTA;candidates=g.89720803_89720804insTG/c.954_955insTG/g.89720803_8972
0804insTG/c.954_955insTG,g.89720804_89720807delACTT/c.955_958delACTT/g.897207
99_89720802delTACT/c.950_953delTACT;1_CandidatesOmitted;dbxref=GeneID:5728,HG
NC:9588,MIM:601728;aliases=NP_000305;source=RefSeq
In this example, both deletion c.950_953delTACT and insertion c.954_955insTA are possible. Both insertion involves fewer nucleotides and is chosen as the most likely inference. Deletion is given in the candidates tag.
The candidates field shows the right-aligned genomic, right-aligned cDNA, left-aligned genomic and left-aligned cDNA identifiers separated by /.
$ transvar panno --ccds -i 'A1BG:p.G132fs*2' --max-candidates 1
A1BG:p.G132fs*2 CCDS12976.1 (protein_coding) A1BG -
chr19:g.58863868delC/c.395delG/p.G132fs*2 inside_[cds_in_exon_4]
CSQN=Frameshift;left_align_cDNA=c.394delG;left_align_gDNA=g.58863867delC;cand
idates=g.58863873delG/c.393delC/g.58863869delG/c.389delC;13_CandidatesOmitted
;source=CCDS
Frameshift variants can be difficult since there might be too many valid underlying nucleotide variants. Suppose we have a relatively long insertion,
$ transvar ganno -i 'chr11:g.32417908_32417909insACCGTACA' --ccds
chr11:g.32417908_32417909insACCGTACA CCDS55750.1 (protein_coding) WT1 -
chr11:g.32417908_32417909insACCGTACA/c.456_457insTGTACGGT/p.A153Cfs*70 inside_[cds_in_exon_6]
CSQN=Frameshift;left_align_gDNA=g.32417908_32417909insACCGTACA;unalign_gDNA=g
.32417908_32417909insACCGTACA;left_align_cDNA=c.456_457insTGTACGGT;unalign_cD
NA=c.456_457insTGTACGGT;source=CCDS
chr11:g.32417908_32417909insACCGTACA CCDS55751.1 (protein_coding) WT1 -
chr11:g.32417908_32417909insACCGTACA/c.507_508insTGTACGGT/p.A170Cfs*70 inside_[cds_in_exon_7]
CSQN=Frameshift;left_align_gDNA=g.32417908_32417909insACCGTACA;unalign_gDNA=g
.32417908_32417909insACCGTACA;left_align_cDNA=c.507_508insTGTACGGT;unalign_cD
NA=c.507_508insTGTACGGT;source=CCDS
chr11:g.32417908_32417909insACCGTACA CCDS44561.1 (protein_coding) WT1 -
chr11:g.32417908_32417909insACCGTACA/c.1092_1093insTGTACGGT/p.A365Cfs*70 inside_[cds_in_exon_6]
CSQN=Frameshift;left_align_gDNA=g.32417908_32417909insACCGTACA;unalign_gDNA=g
.32417908_32417909insACCGTACA;left_align_cDNA=c.1092_1093insTGTACGGT;unalign_
cDNA=c.1092_1093insTGTACGGT;source=CCDS
chr11:g.32417908_32417909insACCGTACA CCDS44562.1 (protein_coding) WT1 -
chr11:g.32417908_32417909insACCGTACA/c.1143_1144insTGTACGGT/p.A382Cfs*70 inside_[cds_in_exon_7]
CSQN=Frameshift;left_align_gDNA=g.32417908_32417909insACCGTACA;unalign_gDNA=g
.32417908_32417909insACCGTACA;left_align_cDNA=c.1143_1144insTGTACGGT;unalign_
cDNA=c.1143_1144insTGTACGGT;source=CCDS
chr11:g.32417908_32417909insACCGTACA CCDS7878.2 (protein_coding) WT1 -
chr11:g.32417908_32417909insACCGTACA/c.1143_1144insTGTACGGT/p.A382Cfs*70 inside_[cds_in_exon_7]
CSQN=Frameshift;left_align_gDNA=g.32417908_32417909insACCGTACA;unalign_gDNA=g
.32417908_32417909insACCGTACA;left_align_cDNA=c.1143_1144insTGTACGGT;unalign_
cDNA=c.1143_1144insTGTACGGT;source=CCDS
But now suppose we only know its protein identifier and forget about the original identifier. Using panno, we can get roughly how the original identifier look like:
$ transvar panno -i 'WT1:p.A170Cfs*70' --ccds --max-candidates 2
would return more than 80 underlying variants. In this case the argument –max-candidates (default to 10) controls the maximum number of candidates output.
WT1:p.A170Cfs*70 CCDS55751.1 (protein_coding) WT1 -
chr11:g.32417908_32417909insTTGGGGCA/c.507_508insTGCCCCAA/p.A170Cfs*70 inside_[cds_in_exons_[7,8,9]]
CSQN=Frameshift;left_align_cDNA=c.507_508insTGCCCCAA;left_align_gDNA=g.324179
08_32417909insTTGGGGCA;candidates=g.32417908_32417909insTTGNNNCA/c.507_508ins
TGNNNCAA/g.32417908_32417909insTTGNNNCA/c.507_508insTGNNNCAA,g.32417908_32417
909insGTGNNNCA/c.507_508insTGNNNCAC/g.32417908_32417909insGTGNNNCA/c.507_508i
nsTGNNNCAC;80_CandidatesOmitted;source=CCDS
Sometimes the alternative amino acid can be missing
$ transvar panno -i ADAMTSL1:p.I396fs*30 --ccds --max-candidates 2
ADAMTSL1:p.I396fs*30 CCDS6485.1 (protein_coding) ADAMTSL1 +
chr9:g.18680360_18680361insG/c.1187_1188insG/p.I396fs*30 inside_[cds_in_exon_11]
CSQN=Frameshift;left_align_cDNA=c.1187_1188insG;left_align_gDNA=g.18680360_18
680361insG;candidates=g.18680359dupA/c.1186dupA/g.18680358_18680359insA/c.118
5_1186insA,g.18680359_18680360insC/c.1186_1187insC/g.18680359_18680360insC/c.
1186_1187insC;11_CandidatesOmitted;source=CCDS
ADAMTSL1:p.I396fs*30 CCDS47954.1 (protein_coding) ADAMTSL1 +
chr9:g.18680360_18680361insG/c.1187_1188insG/p.I396fs*30 inside_[cds_in_exon_11]
CSQN=Frameshift;left_align_cDNA=c.1187_1188insG;left_align_gDNA=g.18680360_18
680361insG;candidates=g.18680359dupA/c.1186dupA/g.18680358_18680359insA/c.118
5_1186insA,g.18680359_18680360insC/c.1186_1187insC/g.18680359_18680360insC/c.
1186_1187insC;11_CandidatesOmitted;source=CCDS
TransVar can also take protein identifiers such as as input. For example,
$ transvar panno --refseq -i 'NP_006266:p.G240Afs*50' --idmap protein_id
NP_006266:p.G240Afs*50 NM_006275.5 (protein_coding) SRSF6 +
chr20:g.42089387delG/c.719delG/p.G240Afs*50 inside_[cds_in_exon_6]
CSQN=Frameshift;left_align_cDNA=c.718delG;left_align_gDNA=g.42089386delG;cand
idates=g.42089385delA/c.717delA/g.42089382delA/c.714delA;dbxref=GeneID:6431,H
GNC:10788,HPRD:09054,MIM:601944;aliases=NP_006266;source=RefSeq
The output gives the exact details of the mutation on the DNA levels, properly right-aligned. The candidates fields also include other equally-likely mutation identifiers. candidates have the format [right-align-gDNA]/[right-align-cDNA]/[left-align-gDNA]/[left-align-cDNA] for each hit and , separation between hits.
Similar applies when the underlying mutation is an insertion. TransVar can infer insertion sequence of under 3 base pairs long. For example,
$ transvar panno -i 'AASS:p.I355Mfs*10' --ccds --max-candidates 1
AASS:p.I355Mfs*10 CCDS5783.1 (protein_coding) AASS -
chr7:g.121753753_121753754insTC/c.1064_1065insGA/p.I355Mfs*10 inside_[cds_in_exon_9]
CSQN=Frameshift;left_align_cDNA=c.1064_1065insGA;left_align_gDNA=g.121753753_
121753754insTC;candidates=g.121753753_121753754insGC/c.1064_1065insGC/g.12175
3753_121753754insGC/c.1064_1065insGC;3_CandidatesOmitted;source=CCDS
When the alternative becomes a stop codon, frameshift mutation becomes a nonsense mutation:
$ transvar panno -i 'APC:p.I1557*fs*3' --ccds
returns a nonsense mutation
APC:p.I1557*fs*3 CCDS4107.1 (protein_coding) APC +
chr5:g.112175960_112175962delATTinsTAA/c.4669_4671delATTinsTAA/p.I1557* inside_[cds_in_exon_15]
CSQN=Nonsense;reference_codon=ATT;candidate_codons=TAA,TAG,TGA;candidate_mnv_
variants=chr5:g.112175960_112175962delATTinsTAG,chr5:g.112175960_112175962del
ATTinsTGA;source=CCDS
Whole transcript¶
TransVar provides an easy way to investigate a whole transcript by supplying the gene id.
$ transvar panno -i 'Dnmt3a' --refseq
outputs the basic information of transcripts of the protein, in an intuitive way,
Dnmt3a XM_005264176.1 (protein_coding) DNMT3A -
chr2:g.25451421_25537541/c.1_2739/p.M1_*913 whole_transcript
promoter=chr2:25537541_25538541;#exons=23;cds=chr2:25457148_25536853
Dnmt3a XM_005264175.1 (protein_coding) DNMT3A -
chr2:g.25451421_25537354/c.1_2739/p.M1_*913 whole_transcript
promoter=chr2:25537354_25538354;#exons=23;cds=chr2:25457148_25536853
Dnmt3a XM_005264177.1 (protein_coding) DNMT3A -
chr2:g.25451421_25475145/c.1_2070/p.M1_*690 whole_transcript
promoter=chr2:25475145_25476145;#exons=18;cds=chr2:25457148_25471091
Dnmt3a NM_175629.2 (protein_coding) DNMT3A -
chr2:g.25455830_25565459/c.1_2739/p.M1_*913 whole_transcript
promoter=chr2:25565459_25566459;#exons=23;cds=chr2:25457148_25536853
Dnmt3a NM_022552.4 (protein_coding) DNMT3A -
chr2:g.25455830_25564784/c.1_2739/p.M1_*913 whole_transcript
promoter=chr2:25564784_25565784;#exons=23;cds=chr2:25457148_25536853
Dnmt3a NM_153759.3 (protein_coding) DNMT3A -
chr2:g.25455830_25475184/c.1_2172/p.M1_*724 whole_transcript
promoter=chr2:25475184_25476184;#exons=19;cds=chr2:25457148_25475066
Dnmt3a NM_175630.1 (protein_coding) DNMT3A -
chr2:g.25504321_25565459/c.1_501/p.M1_*167 whole_transcript
promoter=chr2:25565459_25566459;#exons=4;cds=chr2:25505257_25536853
Search alternative codon identifiers¶
An identifier is regarded as an alternative if the underlying codon overlap with the one from the original identifier. Example: to search alternative identifiers of CDKN2A.p.58 (without knowing reference allele),
$ transvar codonsearch --ccds -i CDKN2A:p.58
origin_id alt_id chrm codon1 codon2 transcripts_choice
CDKN2A:p.58 CDKN2A.p.73 chr9 21971184-21971185-21971186
21971182-21971183-21971184 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
CDKN2A:p.58 CDKN2A.p.72 chr9 21971184-21971185-21971186
21971185-21971186-21971187 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
The pair of transcript id listed corresponds to the transcripts based on which, the original and alternative identifiers are defined. Multiple pairs of transcript definitions are appended following a ,.
Example: to search alternative identifiers of DHODH:G152R (knowing reference allele G, alternative allele here will be ignored),
$ transvar codonsearch -i DHODH:G152R --refseq
outputs
origin_id alt_id chrm codon1 codon2 transcripts_choice
DHODH:G152R DHODH.p.G124 chr16 72050942-72050943-72050944
72050942-72050943-72050944 NM_001361[RefSeq]/XM_005255827[RefSeq]
DHODH:G152R DHODH.p.G16 chr16 72050942-72050943-72050944
72050942-72050943-72050944 NM_001361[RefSeq]/XM_005255828[RefSeq]
DHODH:G152R DHODH.p.G9 chr16 72050942-72050943-72050944
72050942-72050943-72050944 NM_001361[RefSeq]/XM_005255829[RefSeq]
TransVar outputs genomic positions of codons based on original transcript (4th column in the output) and alternative transcript (5th column in the output). The potential transcript usages are also appended.
Example: to run transvar codonsearch to batch process a list of mutation identifiers.
$ transvar codonsearch -l example/input_table2 --ccds -m 1 -o 1
Example input table
origin_id alt_id chrm codon1 codon2 transcripts_choice
CDKN2A:p.61 CDKN2A.p.76 chr9 21971175-21971176-21971177
21971173-21971174-21971175 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
CDKN2A:p.61 CDKN2A.p.75 chr9 21971175-21971176-21971177
21971176-21971177-21971178 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
CDKN2A:p.69 CDKN2A.p.84 chr9 21971151-21971152-21971153
21971149-21971150-21971151 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
CDKN2A:p.69 CDKN2A.p.83 chr9 21971151-21971152-21971153
21971152-21971153-21971154 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
CDKN2A:p.69 CDKN2A.p.55 chr9 21971194-21971195-21971196
21971193-21971194-21971195 CCDS6511[CCDS]/CCDS6510[CCDS],CCDS6511[CCDS]/CCDS56565[CCDS]
CDKN2A:p.69 CDKN2A.p.54 chr9 21971194-21971195-21971196
21971196-21971197-21971198 CCDS6511[CCDS]/CCDS6510[CCDS],CCDS6511[CCDS]/CCDS56565[CCDS]
ERBB2:p.755 ERBB2.p.725 chr17 37880219-37880220-37880221
37880219-37880220-37880221 CCDS32642[CCDS]/CCDS45667[CCDS]
ERBB2:p.755 ERBB2.p.785 chr17 37881024-37881025-37881026
37881024-37881025-37881026 CCDS45667[CCDS]/CCDS32642[CCDS]
outputs
origin_id alt_id chrm codon1
codon2 transcripts_choice
CDKN2A:p.61 CDKN2A.p.76 chr9 21971175-21971176-21971177
21971173-21971174-21971175 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
CDKN2A:p.61 CDKN2A.p.75 chr9 21971175-21971176-21971177
21971176-21971177-21971178 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
CDKN2A:p.69 CDKN2A.p.54 chr9 21971194-21971195-21971196
21971196-21971197-21971198 CCDS6511[CCDS]/CCDS6510[CCDS],CCDS6511[CCDS]/CCDS56565[CCDS]
CDKN2A:p.69 CDKN2A.p.55 chr9 21971194-21971195-21971196
21971193-21971194-21971195 CCDS6511[CCDS]/CCDS6510[CCDS],CCDS6511[CCDS]/CCDS56565[CCDS]
CDKN2A:p.69 CDKN2A.p.83 chr9 21971151-21971152-21971153
21971152-21971153-21971154 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
CDKN2A:p.69 CDKN2A.p.84 chr9 21971151-21971152-21971153
21971149-21971150-21971151 CCDS6510[CCDS]/CCDS6511[CCDS],CCDS56565[CCDS]/CCDS6511[CCDS]
ERBB2:p.755 ERBB2.p.785 chr17 37881024-37881025-37881026
37881024-37881025-37881026 CCDS45667[CCDS]/CCDS32642[CCDS]
ERBB2:p.755 ERBB2.p.725 chr17 37880219-37880220-37880221
37880219-37880220-37880221 CCDS32642[CCDS]/CCDS45667[CCDS]
The third column indicates the potential transcript usage for the alternative identifier. Each transcript usage is denoted by <listing transcript>/<actual transcript>. Different potential choices are separated by ‘,’.
Infer potential codon identity¶
Example: to check if MET.p1010 and MET.p992 may be refering to one mutation due to different usage of transcripts,
$ transvar codonsearch --refseq -i MET:p.1010
gives
origin_id alt_id chrm codon1 codon2 transcripts_choice
MET:p.1010 MET.p.973 chr7 116411932-116411933-116411934
116411932-116411933-116411934 XM_005250353[RefSeq]/NM_000245[RefSeq]
MET:p.1010 MET.p.991 chr7 116411932-116411933-116411934
116411932-116411933-116411934 XM_005250353[RefSeq]/NM_001127500[RefSeq]
MET:p.1010 MET.p.543 chr7 116411932-116411933-116411934
116411932-116411933-116411934 XM_005250353[RefSeq]/XM_005250354[RefSeq]
MET:p.1010 MET.p.1029 chr7 116411989-116411990-116411991
116411989-116411990-116411991 NM_001127500[RefSeq]/XM_005250353[RefSeq]
MET:p.1010 MET.p.992 chr7 116411989-116411990-116411991
116411989-116411990-116411991 NM_001127500[RefSeq]/NM_000245[RefSeq]
MET:p.1010 MET.p.562 chr7 116411989-116411990-116411991
116411989-116411990-116411991 NM_001127500[RefSeq]/XM_005250354[RefSeq]
MET:p.1010 MET.p.1047 chr7 116412043-116414935-116414936
116412043-116414935-116414936 NM_000245[RefSeq]/XM_005250353[RefSeq]
MET:p.1010 MET.p.1028 chr7 116412043-116414935-116414936
116412043-116414935-116414936 NM_000245[RefSeq]/NM_001127500[RefSeq]
MET:p.1010 MET.p.580 chr7 116412043-116414935-116414936
116412043-116414935-116414936 NM_000245[RefSeq]/XM_005250354[RefSeq]
Since MET.p.992 is in the list, the two identifiers might be due to the same genomic mutation.