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Annotation From Protein Level

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Wanding Zhou edited this page Mar 20, 2016 · 17 revisions

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 --uniprot option to TransVar. For example,

$ transvar panno --ccds -i 'Q5VUM1:47' --uniprot
Q5VUM1:47	CCDS4972 (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' --uniprot --ccds
P28222:p.146_148refDRY	CCDS4986 (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 (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 range

$ transvar panno --ccds -i 'ABCB11:p.200_400'

outputs

ABCB11:p.200_400	CCDS46444 (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

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 (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 (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 (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 (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 (protein_coding)	ABCC3	+
   chr17:g.48745254_48745259delinsAGGAGGAGG/c.1666_1671delinsAGGAGGAGG/p.Y556_V557delinsRRR	inside_[cds_in_exon_13]
   CSQN=MultiAAMissense;216_CandidatesOmitted;source=CCDS

Frame-shift variants

$ transvar panno --ccds -i 'A1BG:p.G132fs*2'

The candidate field shows the right-aligned genomic, right-aligned cDNA, left-aligned genomic and left-aligned cDNA identifiers separated by /.

A1BG:p.G132fs*2	CCDS12976 (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;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 (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 (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	CCDS7878 (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	CCDS44561 (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 (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

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 (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_32417909insAANNNACA/c.507_508ins
   TGTNNNTT/g.32417908_32417909insAANNNACA/c.507_508insTGTNNNTT,g.32417908_32417
   909insAANNNGCA/c.507_508insTGCNNNTT/g.32417908_32417909insAANNNGCA/c.507_508i
   nsTGCNNNTT,g.32417908_32417909insACNNNACA/c.507_508insTGTNNNGT/g.32417908_324
   17909insACNNNACA/c.507_508insTGTNNNGT,g.32417908_32417909insACNNNGCA/c.507_50
   8insTGCNNNGT/g.32417908_32417909insACNNNGCA/c.507_508insTGCNNNGT,g.32417908_3
   2417909insAGNNNACA/c.507_508insTGTNNNCT/g.32417908_32417909insAGNNNACA/c.507_
   508insTGTNNNCT,g.32417908_32417909insAGNNNGCA/c.507_508insTGCNNNCT/g.32417908
   _32417909insAGNNNGCA/c.507_508insTGCNNNCT,g.32417908_32417909insATNNNACA/c.50
   7_508insTGTNNNAT/g.32417908_32417909insATNNNACA/c.507_508insTGTNNNAT,g.324179
   08_32417909insATNNNGCA/c.507_508insTGCNNNAT/g.32417908_32417909insATNNNGCA/c.
   507_508insTGCNNNAT,g.32417908_32417909insGANNNACA/c.507_508insTGTNNNTC/g.3241
   7908_32417909insGANNNACA/c.507_508insTGTNNNTC,g.32417908_32417909insGANNNGCA/
   c.507_508insTGCNNNTC/g.32417908_32417909insGANNNGCA/c.507_508insTGCNNNTC;79_C
   andidatesOmitted;source=CCDS

Sometimes the alternative amino acid can be missing

$ transvar panno -i ADAMTSL1:p.I396fs*30 --ccds

TransVar can also take protein identifiers such as as input. For example,

$ transvar panno --refseq -i 'NP_006266.2:p.G240Afs*50'
NP_006266.2:p.G240Afs*50	NM_006275 (protein_coding)	SRSF6	+
   chr20:g.42089385delA/c.717delA/p.G240Afs*50	inside_[cds_in_exon_6]
   CSQN=Frameshift;left_align_cDNA=c.714delA;left_align_gDNA=g.42089382delA;cand
   idates=g.42089387delG/c.719delG/g.42089386delG/c.718delG;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
AASS:p.I355Mfs*10	CCDS5783 (protein_coding)	AASS	-
   chr7:g.121753753_121753754insCC/c.1064_1065insGG/p.I355Mfs*10	inside_[cds_in_exon_9]
   CSQN=Frameshift;left_align_cDNA=c.1064_1065insGG;left_align_gDNA=g.121753753_
   121753754insCC;candidates=g.121753753_121753754insGC/c.1064_1065insGC/g.12175
   3753_121753754insGC/c.1064_1065insGC,g.121753753_121753754insTC/c.1064_1065in
   sGA/g.121753753_121753754insTC/c.1064_1065insGA,g.121753754_121753755insCA/c.
   1064_1065insGT/g.121753753_121753754insAC/c.1063_1064insTG;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 (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 (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 (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 (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 (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 (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 (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 (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.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]
DHODH:G152R	DHODH.p.G124	chr16	72050942-72050943-72050944
   72050942-72050943-72050944	NM_001361[RefSeq]/XM_005255827[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.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]

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

/. 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.562	chr7	116411989-116411990-116411991
   116411989-116411990-116411991	NM_001127500[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.973	chr7	116411932-116411933-116411934
   116411932-116411933-116411934	XM_005250353[RefSeq]/NM_000245[RefSeq]
MET:p.1010	MET.p.580	chr7	116412043-116414935-116414936
   116412043-116414935-116414936	NM_000245[RefSeq]/XM_005250354[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.1028	chr7	116412043-116414935-116414936
   116412043-116414935-116414936	NM_000245[RefSeq]/NM_001127500[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.1047	chr7	116412043-116414935-116414936
   116412043-116414935-116414936	NM_000245[RefSeq]/XM_005250353[RefSeq]

Since MET.p.992 is in the list, the two identifiers might be due to the same genomic mutation.

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