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: ENST00000389672
Querying Taster for transcript #2: ENST00000514100
Querying Taster for transcript #3: ENST00000502694
MT speed 0 s - this script 3.9789 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EPHA6polymorphism_automatic3.28004290395256e-12simple_aaeE346Ksingle base exchangers301948show file
EPHA6polymorphism_automatic4.68162517974768e-07without_aaesingle base exchangers301948show file
EPHA6polymorphism_automatic4.68162517974768e-07without_aaesingle base exchangers301948show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999999999672 (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
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:97365038G>AN/A show variant in all transcripts   IGV
HGNC symbol EPHA6
Ensembl transcript ID ENST00000514100
Genbank transcript ID N/A
UniProt peptide Q9UF33
alteration type single base exchange
alteration region CDS
DNA changes c.1036G>A
cDNA.1278G>A
g.831614G>A
AA changes E346K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 346
frameshift no
known variant Reference ID: rs301948
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC236328715234
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1180
0.0220.001
(flanking)1.7070.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased831606wt: 0.8666 / mu: 0.9101 (marginal change - not scored)wt: GTGTGAGCAGTGCGA
mu: GTGTGAGCAGTGCAA		 GTGA|gcag
Donor marginally increased831615wt: 0.9262 / mu: 0.9697 (marginal change - not scored)wt: GTGCGAGTCCAGCTC
mu: GTGCAAGTCCAGCTC		 GCGA|gtcc
Donor marginally increased831610wt: 0.9416 / mu: 0.9872 (marginal change - not scored)wt: GAGCAGTGCGAGTCC
mu: GAGCAGTGCAAGTCC		 GCAG|tgcg
distance from splice site 76
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      346EDGLESLCEQCESSSGYGTGLVLM
mutated  all conserved    346EDGLESLCEQCKSSSGYGTGLVL
Ptroglodytes  no alignment  ENSPTRG00000015134  n/a
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000055540  n/a
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000003966  n/a
Drerio  no alignment  ENSDARG00000022971  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000017584  305DVVYNVLCKKCDP
protein features
start (aa)end (aa)featuredetails 
23549TOPO_DOMExtracellular (Potential).lost
330434DOMAINFibronectin type-III 1.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1197 / 1197
position (AA) of stopcodon in wt / mu AA sequence 399 / 399
position of stopcodon in wt / mu cDNA 1439 / 1439
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 243 / 243
chromosome 3
strand 1
last intron/exon boundary 1395
theoretical NMD boundary in CDS 1102
length of CDS 1197
coding sequence (CDS) position 1036
cDNA position
(for ins/del: last normal base / first normal base)		 1278
gDNA position
(for ins/del: last normal base / first normal base)		 831614
chromosomal position
(for ins/del: last normal base / first normal base)		 97365038
original gDNA sequence snippet AAAGCTTGTGTGAGCAGTGCGAGTCCAGCTCTGGTTATGGT
altered gDNA sequence snippet AAAGCTTGTGTGAGCAGTGCAAGTCCAGCTCTGGTTATGGT
original cDNA sequence snippet AAAGCTTGTGTGAGCAGTGCGAGTCCAGCTCTGGTTATGGT
altered cDNA sequence snippet AAAGCTTGTGTGAGCAGTGCAAGTCCAGCTCTGGTTATGGT
wildtype AA sequence MKDSPFQVTK LYWLNEKWDF IASASDMAAE QGQILVIATA AVGGFTLLVI LTLFFLITGR
CQWYIKAKMK SEEKRRNHLQ NGHLRFPGIK TYIDPDTYED PSLAVHEFAK EIDPSRIRIE
RVIGAGEFGE VCSGRLKTPG KREIPVAIKT LKGGHMDRQR RDFLREASIM GQFDHPNIIR
LEGVVTKRSF PAIGVEAFCP SFLRAGFLNS IQAPHPVPGG GSLPPRIPAG RPVMIVVEYM
ENGSLDSFLR KHDGHFTVIQ LVGMLRGIAS GMKYLSDMGY VHRDLAARNI LVNSNLVCKV
SDFGLSRVLE DDPEAAYTTT RPTNHNKEQS ELVKEDGLES LCEQCESSSG YGTGLVLMWK
RNRRAMGASG QTRKQCDKRD NPPTDLFQTL TLNLCYSA*
mutated AA sequence MKDSPFQVTK LYWLNEKWDF IASASDMAAE QGQILVIATA AVGGFTLLVI LTLFFLITGR
CQWYIKAKMK SEEKRRNHLQ NGHLRFPGIK TYIDPDTYED PSLAVHEFAK EIDPSRIRIE
RVIGAGEFGE VCSGRLKTPG KREIPVAIKT LKGGHMDRQR RDFLREASIM GQFDHPNIIR
LEGVVTKRSF PAIGVEAFCP SFLRAGFLNS IQAPHPVPGG GSLPPRIPAG RPVMIVVEYM
ENGSLDSFLR KHDGHFTVIQ LVGMLRGIAS GMKYLSDMGY VHRDLAARNI LVNSNLVCKV
SDFGLSRVLE DDPEAAYTTT RPTNHNKEQS ELVKEDGLES LCEQCKSSSG YGTGLVLMWK
RNRRAMGASG QTRKQCDKRD NPPTDLFQTL TLNLCYSA*
speed 1.18 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: 0.999999531837482 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:97365038G>AN/A show variant in all transcripts   IGV
HGNC symbol EPHA6
Ensembl transcript ID ENST00000389672
Genbank transcript ID NM_001080448
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.831614G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs301948
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC236328715234
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1180
0.0220.001
(flanking)1.7070.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased831606wt: 0.8666 / mu: 0.9101 (marginal change - not scored)wt: GTGTGAGCAGTGCGA
mu: GTGTGAGCAGTGCAA		 GTGA|gcag
Donor marginally increased831615wt: 0.9262 / mu: 0.9697 (marginal change - not scored)wt: GTGCGAGTCCAGCTC
mu: GTGCAAGTCCAGCTC		 GCGA|gtcc
Donor marginally increased831610wt: 0.9416 / mu: 0.9872 (marginal change - not scored)wt: GAGCAGTGCGAGTCC
mu: GAGCAGTGCAAGTCC		 GCAG|tgcg
distance from splice site 8112
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 39 / 39
chromosome 3
strand 1
last intron/exon boundary 3317
theoretical NMD boundary in CDS 3228
length of CDS 3393
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)		 831614
chromosomal position
(for ins/del: last normal base / first normal base)		 97365038
original gDNA sequence snippet AAAGCTTGTGTGAGCAGTGCGAGTCCAGCTCTGGTTATGGT
altered gDNA sequence snippet AAAGCTTGTGTGAGCAGTGCAAGTCCAGCTCTGGTTATGGT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MQFPSPPAAR SSPAPQAASS SEAAAPATGQ PGPSCPVPGT SRRGRPGTPP AGRVEEEEEE
EEEDVDKDPH PTQNTCLRCR HFSLRERKRE PRRTMGGCEV REFLLQFGFF LPLLTAWPGD
CSHVSNNQVV LLDTTTVLGE LGWKTYPLNG WDAITEMDEH NRPIHTYQVC NVMEPNQNNW
LRTNWISRDA AQKIYVEMKF TLRDCNSIPW VLGTCKETFN LFYMESDESH GIKFKPNQYT
KIDTIAADES FTQMDLGDRI LKLNTEIREV GPIERKGFYL AFQDIGACIA LVSVRVFYKK
CPFTVRNLAM FPDTIPRVDS SSLVEVRGSC VKSAEERDTP KLYCGADGDW LVPLGRCICS
TGYEEIEGSC HACRPGFYKA FAGNTKCSKC PPHSLTYMEA TSVCQCEKGY FRAEKDPPSM
ACTRPPSAPR NVVFNINETA LILEWSPPSD TGGRKDLTYS VICKKCGLDT SQCEDCGGGL
RFIPRHTGLI NNSVIVLDFV SHVNYTFEIE AMNGVSELSF SPKPFTAITV TTDQDAPSLI
GVVRKDWASQ NSIALSWQAP AFSNGAILDY EIKYYEKEHE QLTYSSTRSK APSVIITGLK
PATKYVFHIR VRTATGYSGY SQKFEFETGD ETSDMAAEQG QILVIATAAV GGFTLLVILT
LFFLITGRCQ WYIKAKMKSE EKRRNHLQNG HLRFPGIKTY IDPDTYEDPS LAVHEFAKEI
DPSRIRIERV IGAGEFGEVC SGRLKTPGKR EIPVAIKTLK GGHMDRQRRD FLREASIMGQ
FDHPNIIRLE GVVTKRSFPA IGVEAFCPSF LRAGFLNSIQ APHPVPGGGS LPPRIPAGRP
VMIVVEYMEN GSLDSFLRKH DGHFTVIQLV GMLRGIASGM KYLSDMGYVH RDLAARNILV
NSNLVCKVSD FGLSRVLEDD PEAAYTTTGG KIPIRWTAPE AIAYRKFSSA SDAWSYGIVM
WEVMSYGERP YWEMSNQDVI LSIEEGYRLP APMGCPASLH QLMLHCWQKE RNHRPKFTDI
VSFLDKLIRN PSALHTLVED ILVMPESPGE VPEYPLFVTV GDWLDSIKMG QYKNNFVAAG
FTTFDLISRM SIDDIRRIGV ILIGHQRRIV SSIQTLRLHM MHIQEKGFHV *
mutated AA sequence N/A
speed 0.92 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: 0.999999531837482 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:97365038G>AN/A show variant in all transcripts   IGV
HGNC symbol EPHA6
Ensembl transcript ID ENST00000502694
Genbank transcript ID NM_173655
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.831614G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs301948
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC236328715234
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1180
0.0220.001
(flanking)1.7070.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased831606wt: 0.8666 / mu: 0.9101 (marginal change - not scored)wt: GTGTGAGCAGTGCGA
mu: GTGTGAGCAGTGCAA		 GTGA|gcag
Donor marginally increased831615wt: 0.9262 / mu: 0.9697 (marginal change - not scored)wt: GTGCGAGTCCAGCTC
mu: GTGCAAGTCCAGCTC		 GCGA|gtcc
Donor marginally increased831610wt: 0.9416 / mu: 0.9872 (marginal change - not scored)wt: GAGCAGTGCGAGTCC
mu: GAGCAGTGCAAGTCC		 GCAG|tgcg
distance from splice site 2092
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 331 / 331
chromosome 3
strand 1
last intron/exon boundary 1291
theoretical NMD boundary in CDS 910
length of CDS 1005
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)		 831614
chromosomal position
(for ins/del: last normal base / first normal base)		 97365038
original gDNA sequence snippet AAAGCTTGTGTGAGCAGTGCGAGTCCAGCTCTGGTTATGGT
altered gDNA sequence snippet AAAGCTTGTGTGAGCAGTGCAAGTCCAGCTCTGGTTATGGT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MKDSPFQVTK LYWLNEKWDF IASASDMAAE QGQILVIATA AVGGFTLLVI LTLFFLITGR
CQWYIKAKMK SEEKRRNHLQ NGHLRFPGIK TYIDPDTYED PSLAVHEFAK EIDPSRIRIE
RVIGAGEFGE VCSGRLKTPG KREIPVAIKT LKGGHMDRQR RDFLREASIM GQFDHPNIIR
LEGVVTKRSF PAIGVEAFCP SFLRAGFLNS IQAPHPVPGG GSLPPRIPAG RPVMIVVEYM
ENGSLDSFLR KHDGHFTVIQ LVGMLRGIAS GMKYLSDMGY VHRDLAARNI LVNSNLVCKV
SDFGLSRVLE DDPEAAYTTT DLFQTLTLNL CYSA*
mutated AA sequence N/A
speed 0.83 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