Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000393330
Querying Taster for transcript #2: ENST00000247829
Querying Taster for transcript #3: ENST00000546561
MT speed 0 s - this script 3.106916 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TSPAN8polymorphism_automatic0.99999794107148simple_aaeaffectedG73Asingle base exchangers3763978show file
TSPAN8polymorphism_automatic0.99999794107148simple_aaeaffectedG73Asingle base exchangers3763978show file
TSPAN8polymorphism_automatic0.99999794107148simple_aaeaffectedG73Asingle base exchangers3763978show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.05892852042412e-06 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:71533534C>GN/A show variant in all transcripts   IGV
HGNC symbol TSPAN8
Ensembl transcript ID ENST00000393330
Genbank transcript ID N/A
UniProt peptide P19075
alteration type single base exchange
alteration region CDS
DNA changes c.218G>C
cDNA.771G>C
g.302145G>C
AA changes G73A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 73
frameshift no
known variant Reference ID: rs3763978
databasehomozygous (G/G)heterozygousallele carriers
1000G171795966
ExAC75411768525226
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2630.987
4.4851
(flanking)4.4851
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased302142wt: 0.38 / mu: 0.54wt: CATCATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAA
mu: CATCATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAA		 tcct|GGGA
Acc marginally increased302143wt: 0.4208 / mu: 0.4386 (marginal change - not scored)wt: ATCATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAAA
mu: ATCATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAA		 cctg|GGAT
Acc gained3021520.57mu: CTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAGAAAGTCG ctgc|GGTG
Acc gained3021470.81mu: TGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAGAA gcat|GCTG
Donor gained3021500.31mu: CATGCTGCGGTGCTA TGCT|gcgg
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      73VGAIIMILGFLGCCGAIKESRCML
mutated  not conserved    73VGAIIMILGFLACCGAIKESRCM
Ptroglodytes  all identical  ENSPTRG00000005222  73VGAIIMILGFLGCCGAIKESRCM
Mmulatta  all identical  ENSMMUG00000006469  73VGAIIMIMGFLGCCGAIKESRCM
Fcatus  all identical  ENSFCAG00000013914  53VGSVIMILGFLGCCGAVKE
Mmusculus  all identical  ENSMUSG00000034127  73VGSIIMVLGFLGCCGAVKESRCM
Ggallus  all identical  ENSGALG00000010152  71VGSIIMILGFLGCCGAIKESRCM
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026807  71VGAIIMVLGFFGCCGAIRESRCL
protein features
start (aa)end (aa)featuredetails 
5872TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7383TOPO_DOMCytoplasmic (Potential).lost
84109TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
110205TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
118118CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
206230TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
231237TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 714 / 714
position (AA) of stopcodon in wt / mu AA sequence 238 / 238
position of stopcodon in wt / mu cDNA 1267 / 1267
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 554 / 554
chromosome 12
strand -1
last intron/exon boundary 1214
theoretical NMD boundary in CDS 610
length of CDS 714
coding sequence (CDS) position 218
cDNA position
(for ins/del: last normal base / first normal base)		 771
gDNA position
(for ins/del: last normal base / first normal base)		 302145
chromosomal position
(for ins/del: last normal base / first normal base)		 71533534
original gDNA sequence snippet CATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAAAAG
altered gDNA sequence snippet CATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAG
original cDNA sequence snippet CATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAAAAG
altered cDNA sequence snippet CATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAG
wildtype AA sequence MAGVSACIKY SMFTFNFLFW LCGILILALA IWVRVSNDSQ AIFGSEDVGS SSYVAVDILI
AVGAIIMILG FLGCCGAIKE SRCMLLLFFI GLLLILLLQV ATGILGAVFK SKSDRIVNET
LYENTKLLSA TGESEKQFQE AIIVFQEEFK CCGLVNGAAD WGNNFQHYPE LCACLDKQRP
CQSYNGKQVY KETCISFIKD FLAKNLIIVI GISFGLAVIE ILGLVFSMVL YCQIGNK*
mutated AA sequence MAGVSACIKY SMFTFNFLFW LCGILILALA IWVRVSNDSQ AIFGSEDVGS SSYVAVDILI
AVGAIIMILG FLACCGAIKE SRCMLLLFFI GLLLILLLQV ATGILGAVFK SKSDRIVNET
LYENTKLLSA TGESEKQFQE AIIVFQEEFK CCGLVNGAAD WGNNFQHYPE LCACLDKQRP
CQSYNGKQVY KETCISFIKD FLAKNLIIVI GISFGLAVIE ILGLVFSMVL YCQIGNK*
speed 0.56 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.05892852042412e-06 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:71533534C>GN/A show variant in all transcripts   IGV
HGNC symbol TSPAN8
Ensembl transcript ID ENST00000247829
Genbank transcript ID NM_004616
UniProt peptide P19075
alteration type single base exchange
alteration region CDS
DNA changes c.218G>C
cDNA.497G>C
g.302145G>C
AA changes G73A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 73
frameshift no
known variant Reference ID: rs3763978
databasehomozygous (G/G)heterozygousallele carriers
1000G171795966
ExAC75411768525226
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2630.987
4.4851
(flanking)4.4851
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased302142wt: 0.38 / mu: 0.54wt: CATCATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAA
mu: CATCATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAA		 tcct|GGGA
Acc marginally increased302143wt: 0.4208 / mu: 0.4386 (marginal change - not scored)wt: ATCATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAAA
mu: ATCATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAA		 cctg|GGAT
Acc gained3021520.57mu: CTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAGAAAGTCG ctgc|GGTG
Acc gained3021470.81mu: TGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAGAA gcat|GCTG
Donor gained3021500.31mu: CATGCTGCGGTGCTA TGCT|gcgg
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      73VGAIIMILGFLGCCGAIKESRCML
mutated  not conserved    73VGAIIMILGFLACCGAIKESRCM
Ptroglodytes  all identical  ENSPTRG00000005222  73VGAIIMILGFLGCCGAIKESRCM
Mmulatta  all identical  ENSMMUG00000006469  73VGAIIMIMGFLGCCGAIKESRCM
Fcatus  all identical  ENSFCAG00000013914  53VGSVIMILGFLGCCGAVKE
Mmusculus  all identical  ENSMUSG00000034127  73VGSIIMVLGFLGCCGAVKESRCM
Ggallus  all identical  ENSGALG00000010152  71VGSIIMILGFLGCCGAIKESRCM
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026807  71VGAIIMVLGFFGCCGAIRESRCL
protein features
start (aa)end (aa)featuredetails 
5872TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7383TOPO_DOMCytoplasmic (Potential).lost
84109TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
110205TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
118118CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
206230TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
231237TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 714 / 714
position (AA) of stopcodon in wt / mu AA sequence 238 / 238
position of stopcodon in wt / mu cDNA 993 / 993
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 280 / 280
chromosome 12
strand -1
last intron/exon boundary 940
theoretical NMD boundary in CDS 610
length of CDS 714
coding sequence (CDS) position 218
cDNA position
(for ins/del: last normal base / first normal base)		 497
gDNA position
(for ins/del: last normal base / first normal base)		 302145
chromosomal position
(for ins/del: last normal base / first normal base)		 71533534
original gDNA sequence snippet CATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAAAAG
altered gDNA sequence snippet CATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAG
original cDNA sequence snippet CATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAAAAG
altered cDNA sequence snippet CATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAG
wildtype AA sequence MAGVSACIKY SMFTFNFLFW LCGILILALA IWVRVSNDSQ AIFGSEDVGS SSYVAVDILI
AVGAIIMILG FLGCCGAIKE SRCMLLLFFI GLLLILLLQV ATGILGAVFK SKSDRIVNET
LYENTKLLSA TGESEKQFQE AIIVFQEEFK CCGLVNGAAD WGNNFQHYPE LCACLDKQRP
CQSYNGKQVY KETCISFIKD FLAKNLIIVI GISFGLAVIE ILGLVFSMVL YCQIGNK*
mutated AA sequence MAGVSACIKY SMFTFNFLFW LCGILILALA IWVRVSNDSQ AIFGSEDVGS SSYVAVDILI
AVGAIIMILG FLACCGAIKE SRCMLLLFFI GLLLILLLQV ATGILGAVFK SKSDRIVNET
LYENTKLLSA TGESEKQFQE AIIVFQEEFK CCGLVNGAAD WGNNFQHYPE LCACLDKQRP
CQSYNGKQVY KETCISFIKD FLAKNLIIVI GISFGLAVIE ILGLVFSMVL YCQIGNK*
speed 0.58 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 2.05892852042412e-06 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:71533534C>GN/A show variant in all transcripts   IGV
HGNC symbol TSPAN8
Ensembl transcript ID ENST00000546561
Genbank transcript ID N/A
UniProt peptide P19075
alteration type single base exchange
alteration region CDS
DNA changes c.218G>C
cDNA.439G>C
g.302145G>C
AA changes G73A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 73
frameshift no
known variant Reference ID: rs3763978
databasehomozygous (G/G)heterozygousallele carriers
1000G171795966
ExAC75411768525226
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2630.987
4.4851
(flanking)4.4851
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased302142wt: 0.38 / mu: 0.54wt: CATCATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAA
mu: CATCATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAA		 tcct|GGGA
Acc marginally increased302143wt: 0.4208 / mu: 0.4386 (marginal change - not scored)wt: ATCATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAAA
mu: ATCATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAA		 cctg|GGAT
Acc gained3021520.57mu: CTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAGAAAGTCG ctgc|GGTG
Acc gained3021470.81mu: TGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAGAA gcat|GCTG
Donor gained3021500.31mu: CATGCTGCGGTGCTA TGCT|gcgg
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      73VGAIIMILGFLGCCGAIKESRCML
mutated  not conserved    73VGAIIMILGFLACCGAIKESRCM
Ptroglodytes  all identical  ENSPTRG00000005222  73VGAIIMILGFLGCCGAIKESRCM
Mmulatta  all identical  ENSMMUG00000006469  73VGAIIMIMGFLGCCGAIKESRCM
Fcatus  all identical  ENSFCAG00000013914  53VGSVIMILGFLGCCGAVKE
Mmusculus  all identical  ENSMUSG00000034127  73VGSIIMVLGFLGCCGAVKESRCM
Ggallus  all identical  ENSGALG00000010152  71VGSIIMILGFLGCCGAIKESRCM
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026807  71VGAIIMVLGFFGCCGAIRESRCL
protein features
start (aa)end (aa)featuredetails 
5872TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7383TOPO_DOMCytoplasmic (Potential).lost
84109TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
110205TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
118118CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
206230TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
231237TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 714 / 714
position (AA) of stopcodon in wt / mu AA sequence 238 / 238
position of stopcodon in wt / mu cDNA 935 / 935
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 222 / 222
chromosome 12
strand -1
last intron/exon boundary 882
theoretical NMD boundary in CDS 610
length of CDS 714
coding sequence (CDS) position 218
cDNA position
(for ins/del: last normal base / first normal base)		 439
gDNA position
(for ins/del: last normal base / first normal base)		 302145
chromosomal position
(for ins/del: last normal base / first normal base)		 71533534
original gDNA sequence snippet CATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAAAAG
altered gDNA sequence snippet CATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAG
original cDNA sequence snippet CATGATTCTGGGCTTCCTGGGATGCTGCGGTGCTATAAAAG
altered cDNA sequence snippet CATGATTCTGGGCTTCCTGGCATGCTGCGGTGCTATAAAAG
wildtype AA sequence MAGVSACIKY SMFTFNFLFW LCGILILALA IWVRVSNDSQ AIFGSEDVGS SSYVAVDILI
AVGAIIMILG FLGCCGAIKE SRCMLLLFFI GLLLILLLQV ATGILGAVFK SKSDRIVNET
LYENTKLLSA TGESEKQFQE AIIVFQEEFK CCGLVNGAAD WGNNFQHYPE LCACLDKQRP
CQSYNGKQVY KETCISFIKD FLAKNLIIVI GISFGLAVIE ILGLVFSMVL YCQIGNK*
mutated AA sequence MAGVSACIKY SMFTFNFLFW LCGILILALA IWVRVSNDSQ AIFGSEDVGS SSYVAVDILI
AVGAIIMILG FLACCGAIKE SRCMLLLFFI GLLLILLLQV ATGILGAVFK SKSDRIVNET
LYENTKLLSA TGESEKQFQE AIIVFQEEFK CCGLVNGAAD WGNNFQHYPE LCACLDKQRP
CQSYNGKQVY KETCISFIKD FLAKNLIIVI GISFGLAVIE ILGLVFSMVL YCQIGNK*
speed 0.49 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

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