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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000336596
Querying Taster for transcript #2: ENST00000494014
MT speed 0 s - this script 3.747405 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EPHA3polymorphism_automatic5.2871974452029e-05simple_aaeaffectedW924Rsingle base exchangers35124509show file
EPHA3polymorphism_automatic1without_aaeaffectedsingle base exchangers35124509show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999947128025548 (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) chr3:89521693T>CN/A show variant in all transcripts   IGV
HGNC symbol EPHA3
Ensembl transcript ID ENST00000336596
Genbank transcript ID NM_005233
UniProt peptide P29320
alteration type single base exchange
alteration region CDS
DNA changes c.2770T>C
cDNA.2995T>C
g.365020T>C
AA changes W924R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 924
frameshift no
known variant Reference ID: rs35124509
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC93661403523401
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.540.988
1.3950.999
(flanking)4.1271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased365020wt: 0.37 / mu: 0.72wt: GTGTCTGGACAGCAC
mu: GTGTCCGGACAGCAC		 GTCT|ggac
Donor increased365011wt: 0.45 / mu: 0.62wt: GGCTTAATGGTGTCT
mu: GGCTTAATGGTGTCC		 CTTA|atgg
distance from splice site 77
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      924FRTTGDWLNGVWTAHCKEIFTGVE
mutated  not conserved    924FRTTGDWLNGVRTAHCKEIFTGV
Ptroglodytes  not conserved  ENSPTRG00000015127  924FSTTGDWLNGVRTAHCKEIFTGV
Mmulatta  not conserved  ENSMMUG00000008242  925FRTTGDWLNGVRTAHCKEIFTGV
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000052504  925FHTTGDWLNGMRTAHCKEIFTGV
Ggallus  not conserved  ENSGALG00000015403  924FRTAGDWLNGFRTGQCKGIFTGV
Trubripes  not conserved  ENSTRUG00000001793  945VGTVGDWMDGMRTLPCKEAFSGV
Drerio  not conserved  ENSDARG00000039373  653FHTMGDWLESARTLPCKDA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000020173  903TLQTGPCHDILTGV
protein features
start (aa)end (aa)featuredetails 
566983TOPO_DOMCytoplasmic (Potential).lost
911975DOMAINSAM.lost
937937MOD_RESPhosphotyrosine (By similarity).might get lost (downstream of altered splice site)
981983MOTIFPDZ-binding (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2952 / 2952
position (AA) of stopcodon in wt / mu AA sequence 984 / 984
position of stopcodon in wt / mu cDNA 3177 / 3177
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 226 / 226
chromosome 3
strand 1
last intron/exon boundary 3072
theoretical NMD boundary in CDS 2796
length of CDS 2952
coding sequence (CDS) position 2770
cDNA position
(for ins/del: last normal base / first normal base)		 2995
gDNA position
(for ins/del: last normal base / first normal base)		 365020
chromosomal position
(for ins/del: last normal base / first normal base)		 89521693
original gDNA sequence snippet GTGACTGGCTTAATGGTGTCTGGACAGCACACTGCAAGGAA
altered gDNA sequence snippet GTGACTGGCTTAATGGTGTCCGGACAGCACACTGCAAGGAA
original cDNA sequence snippet GTGACTGGCTTAATGGTGTCTGGACAGCACACTGCAAGGAA
altered cDNA sequence snippet GTGACTGGCTTAATGGTGTCCGGACAGCACACTGCAAGGAA
wildtype AA sequence MDCQLSILLL LSCSVLDSFG ELIPQPSNEV NLLDSKTIQG ELGWISYPSH GWEEISGVDE
HYTPIRTYQV CNVMDHSQNN WLRTNWVPRN SAQKIYVELK FTLRDCNSIP LVLGTCKETF
NLYYMESDDD HGVKFREHQF TKIDTIAADE SFTQMDLGDR ILKLNTEIRE VGPVNKKGFY
LAFQDVGACV ALVSVRVYFK KCPFTVKNLA MFPDTVPMDS QSLVEVRGSC VNNSKEEDPP
RMYCSTEGEW LVPIGKCSCN AGYEERGFMC QACRPGFYKA LDGNMKCAKC PPHSSTQEDG
SMNCRCENNY FRADKDPPSM ACTRPPSSPR NVISNINETS VILDWSWPLD TGGRKDVTFN
IICKKCGWNI KQCEPCSPNV RFLPRQFGLT NTTVTVTDLL AHTNYTFEID AVNGVSELSS
PPRQFAAVSI TTNQAAPSPV LTIKKDRTSR NSISLSWQEP EHPNGIILDY EVKYYEKQEQ
ETSYTILRAR GTNVTISSLK PDTIYVFQIR ARTAAGYGTN SRKFEFETSP DSFSISGESS
QVVMIAISAA VAIILLTVVI YVLIGRFCGY KSKHGADEKR LHFGNGHLKL PGLRTYVDPH
TYEDPTQAVH EFAKELDATN ISIDKVVGAG EFGEVCSGRL KLPSKKEISV AIKTLKVGYT
EKQRRDFLGE ASIMGQFDHP NIIRLEGVVT KSKPVMIVTE YMENGSLDSF LRKHDAQFTV
IQLVGMLRGI ASGMKYLSDM GYVHRDLAAR NILINSNLVC KVSDFGLSRV LEDDPEAAYT
TRGGKIPIRW TSPEAIAYRK FTSASDVWSY GIVLWEVMSY GERPYWEMSN QDVIKAVDEG
YRLPPPMDCP AALYQLMLDC WQKDRNNRPK FEQIVSILDK LIRNPGSLKI ITSAAARPSN
LLLDQSNVDI TTFRTTGDWL NGVWTAHCKE IFTGVEYSSC DTIAKISTDD MKKVGVTVVG
PQKKIISSIK ALETQSKNGP VPV*
mutated AA sequence MDCQLSILLL LSCSVLDSFG ELIPQPSNEV NLLDSKTIQG ELGWISYPSH GWEEISGVDE
HYTPIRTYQV CNVMDHSQNN WLRTNWVPRN SAQKIYVELK FTLRDCNSIP LVLGTCKETF
NLYYMESDDD HGVKFREHQF TKIDTIAADE SFTQMDLGDR ILKLNTEIRE VGPVNKKGFY
LAFQDVGACV ALVSVRVYFK KCPFTVKNLA MFPDTVPMDS QSLVEVRGSC VNNSKEEDPP
RMYCSTEGEW LVPIGKCSCN AGYEERGFMC QACRPGFYKA LDGNMKCAKC PPHSSTQEDG
SMNCRCENNY FRADKDPPSM ACTRPPSSPR NVISNINETS VILDWSWPLD TGGRKDVTFN
IICKKCGWNI KQCEPCSPNV RFLPRQFGLT NTTVTVTDLL AHTNYTFEID AVNGVSELSS
PPRQFAAVSI TTNQAAPSPV LTIKKDRTSR NSISLSWQEP EHPNGIILDY EVKYYEKQEQ
ETSYTILRAR GTNVTISSLK PDTIYVFQIR ARTAAGYGTN SRKFEFETSP DSFSISGESS
QVVMIAISAA VAIILLTVVI YVLIGRFCGY KSKHGADEKR LHFGNGHLKL PGLRTYVDPH
TYEDPTQAVH EFAKELDATN ISIDKVVGAG EFGEVCSGRL KLPSKKEISV AIKTLKVGYT
EKQRRDFLGE ASIMGQFDHP NIIRLEGVVT KSKPVMIVTE YMENGSLDSF LRKHDAQFTV
IQLVGMLRGI ASGMKYLSDM GYVHRDLAAR NILINSNLVC KVSDFGLSRV LEDDPEAAYT
TRGGKIPIRW TSPEAIAYRK FTSASDVWSY GIVLWEVMSY GERPYWEMSN QDVIKAVDEG
YRLPPPMDCP AALYQLMLDC WQKDRNNRPK FEQIVSILDK LIRNPGSLKI ITSAAARPSN
LLLDQSNVDI TTFRTTGDWL NGVRTAHCKE IFTGVEYSSC DTIAKISTDD MKKVGVTVVG
PQKKIISSIK ALETQSKNGP VPV*
speed 0.99 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: without_aae, prob: 8.51550170791687e-17 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr3:89521693T>CN/A show variant in all transcripts   IGV
HGNC symbol EPHA3
Ensembl transcript ID ENST00000494014
Genbank transcript ID N/A
UniProt peptide P29320
alteration type single base exchange
alteration region intron
DNA changes g.365020T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs35124509
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC93661403523401
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.540.988
1.3950.999
(flanking)4.1271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased365020wt: 0.37 / mu: 0.72wt: GTGTCTGGACAGCAC
mu: GTGTCCGGACAGCAC		 GTCT|ggac
Donor increased365011wt: 0.45 / mu: 0.62wt: GGCTTAATGGTGTCT
mu: GGCTTAATGGTGTCC		 CTTA|atgg
distance from splice site 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
566983TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
911975DOMAINSAM.might get lost (downstream of altered splice site)
937937MOD_RESPhosphotyrosine (By similarity).might get lost (downstream of altered splice site)
981983MOTIFPDZ-binding (Potential).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 74 / 74
chromosome 3
strand 1
last intron/exon boundary 2823
theoretical NMD boundary in CDS 2699
length of CDS 2757
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 365020
chromosomal position
(for ins/del: last normal base / first normal base)		 89521693
original gDNA sequence snippet GTGACTGGCTTAATGGTGTCTGGACAGCACACTGCAAGGAA
altered gDNA sequence snippet GTGACTGGCTTAATGGTGTCCGGACAGCACACTGCAAGGAA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDCQLSILLL LSCSVLDSFG ELIPQPSNEV NLLDSKTIQG ELGWISYPSH GWEEISGVDE
HYTPIRTYQV CNVMDHSQNN WLRTNWVPRN SAQKIYVELK FTLRDCNSIP LVLGTCKETF
NLYYMESDDD HGVKFREHQF TKIDTIAADE SFTQMDLGDR ILKLNTEIRE VGPVNKKGFY
LAFQDVGACV ALVSVRVYFK KCPFTVKNLA MFPDTVPMDS QSLVEVRGSC VNNSKEEDPP
RMYCSTEGEW LVPIGKCSCN AGYEERGFMC QACRPGFYKA LDGNMKCAKC PPHSSTQEDG
SMNCRCENNY FRADKDPPSM ACTRPPSSPR NVISNINETS VILDWSWPLD TGGRKDVTFN
IICKKCGWNI KQCEPCSPNV RFLPRQFGLT NTTVTVTDLL AHTNYTFEID AVNGVSELSS
PPRQFAAVSI TTNQAAPSPV LTIKKDRTSR NSISLSWQEP EHPNGIILDY EVKYYEKQEQ
ETSYTILRAR GTNVTISSLK PDTIYVFQIR ARTAAGYGTN SRKFEFETSP DSFSISGESS
QVVMIAISAA VAIILLTVVI YVLIGRFCGY KSKHGADEKR LHFGNGHLKL PGLRTYVDPH
TYEDPTQAVH EFAKELDATN ISIDKVVGAG EFGEVCSGRL KLPSKKEISV AIKTLKVGYT
EKQRRDFLGE ASIMGQFDHP NIIRLEGVVT KSKPVMIVTE YMENGSLDSF LRKHDAQFTV
IQLVGMLRGI ASGMKYLSDM GYVHRDLAAR NILINSNLVC KVSDFGLSRV LEDDPEAAYT
TRGGKIPIRW TSPEAIAYRK FTSASDVWSY GIVLWEVMSY GERPYWEMSN QDVIKAVDEG
YRLPPPMDCP AALYQLMLDC WQKDRNNRPK FEQIVSILDK LIRNPGSLKI ITSAAARPSN
LLLDQSNVDI TTFRTTVT*
mutated AA sequence N/A
speed 0.76 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

Problems