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: ENST00000360428
Querying Taster for transcript #2: ENST00000434452
MT speed 1.29 s - this script 3.000428 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DSC3polymorphism_automatic5.4280530069617e-06simple_aaeaffectedS78Tsingle base exchangers276937show file
DSC3polymorphism_automatic5.4280530069617e-06simple_aaeaffectedS78Tsingle base exchangers276937show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999994571946993 (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) chr18:28611061A>TN/A show variant in all transcripts   IGV
HGNC symbol DSC3
Ensembl transcript ID ENST00000360428
Genbank transcript ID NM_001941
UniProt peptide Q14574
alteration type single base exchange
alteration region CDS
DNA changes c.232T>A
cDNA.313T>A
g.11721T>A
AA changes S78T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 78
frameshift no
known variant Reference ID: rs276937
databasehomozygous (T/T)heterozygousallele carriers
1000G53711041641
ExAC100381269122729
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0610.099
1.1050.122
(flanking)-0.4650.124
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased11718wt: 0.61 / mu: 0.84wt: ATGATGGGTCAGTGT
mu: ATGATGGGACAGTGT		 GATG|ggtc
Donor gained117230.35mu: GGGACAGTGTACACA GACA|gtgt
distance from splice site 78
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      78SDPDFRVLNDGSVYTARAVALSDK
mutated  all conserved    78SDPDFRVLNDGTVYTARAVALSD
Ptroglodytes  all identical  ENSPTRG00000009940  78SDPDFRVLNDGSVYTARAVALSD
Mmulatta  all identical  ENSMMUG00000007668  78GDPDFRVLSDGSVYTARAVVLSD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000059898  78VLDDGSVYPTRAVVLSD
Ggallus  all identical  ENSGALG00000015140  55SDGSFKVLEDGSVYTTS
Trubripes  not conserved  ENSTRUG00000007388  92FAISGAGKIEVAAPMVVSP
Drerio  all identical  ENSDARG00000039677  114GSIVTLRSLVIST
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000004721  77LEDGSIFAQKRISLAG
protein features
start (aa)end (aa)featuredetails 
28135PROPEPPotential. /FTId=PRO_0000003875.lost
136243DOMAINCadherin 1.might get lost (downstream of altered splice site)
136690TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
166166CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
244355DOMAINCadherin 2.might get lost (downstream of altered splice site)
356471DOMAINCadherin 3.might get lost (downstream of altered splice site)
392392CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
472579DOMAINCadherin 4.might get lost (downstream of altered splice site)
546546CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
580690DOMAINCadherin 5.might get lost (downstream of altered splice site)
629629CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
691711TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
712896TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
818818MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
859859MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
863863MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
868868MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2691 / 2691
position (AA) of stopcodon in wt / mu AA sequence 897 / 897
position of stopcodon in wt / mu cDNA 2772 / 2772
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 82 / 82
chromosome 18
strand -1
last intron/exon boundary 2575
theoretical NMD boundary in CDS 2443
length of CDS 2691
coding sequence (CDS) position 232
cDNA position
(for ins/del: last normal base / first normal base)		 313
gDNA position
(for ins/del: last normal base / first normal base)		 11721
chromosomal position
(for ins/del: last normal base / first normal base)		 28611061
original gDNA sequence snippet TCAGAGTTCTAAATGATGGGTCAGTGTACACAGCCAGGGCT
altered gDNA sequence snippet TCAGAGTTCTAAATGATGGGACAGTGTACACAGCCAGGGCT
original cDNA sequence snippet TCAGAGTTCTAAATGATGGGTCAGTGTACACAGCCAGGGCT
altered cDNA sequence snippet TCAGAGTTCTAAATGATGGGACAGTGTACACAGCCAGGGCT
wildtype AA sequence MAAAGPRRSV RGAVCLHLLL TLVIFSRAGE ACKKVILNVP SKLEADKIIG RVNLEECFRS
ADLIRSSDPD FRVLNDGSVY TARAVALSDK KRSFTIWLSD KRKQTQKEVT VLLEHQKKVS
KTRHTRETVL RRAKRRWAPI PCSMQENSLG PFPLFLQQVE SDAAQNYTVF YSISGRGVDK
EPLNLFYIER DTGNLFCTRP VDREEYDVFD LIAYASTADG YSADLPLPLP IRVEDENDNH
PVFTEAIYNF EVLESSRPGT TVGVVCATDR DEPDTMHTRL KYSILQQTPR SPGLFSVHPS
TGVITTVSHY LDREVVDKYS LIMKVQDMDG QFFGLIGTST CIITVTDSND NAPTFRQNAY
EAFVEENAFN VEILRIPIED KDLINTANWR VNFTILKGNE NGHFKISTDK ETNEGVLSVV
KPLNYEENRQ VNLEIGVNNE APFARDIPRV TALNRALVTV HVRDLDEGPE CTPAAQYVRI
KENLAVGSKI NGYKAYDPEN RNGNGLRYKK LHDPKGWITI DEISGSIITS KILDREVETP
KNELYNITVL AIDKDDRSCT GTLAVNIEDV NDNPPEILQE YVVICKPKMG YTDILAVDPD
EPVHGAPFYF SLPNTSPEIS RLWSLTKVND TAARLSYQKN AGFQEYTIPI TVKDRAGQAA
TKLLRVNLCE CTHPTQCRAT SRSTGVILGK WAILAILLGI ALLFSVLLTL VCGVFGATKG
KRFPEDLAQQ NLIISNTEAP GDDRVCSANG FMTQTTNNSS QGFCGTMGSG MKNGGQETIE
MMKGGNQTLE SCRGAGHHHT LDSCRGGHTE VDNCRYTYSE WHSFTQPRLG EKLHRCNQNE
DRMPSQDYVL TYNYEGRGSP AGSVGCCSEK QEEDGLDFLN NLEPKFITLA EACTKR*
mutated AA sequence MAAAGPRRSV RGAVCLHLLL TLVIFSRAGE ACKKVILNVP SKLEADKIIG RVNLEECFRS
ADLIRSSDPD FRVLNDGTVY TARAVALSDK KRSFTIWLSD KRKQTQKEVT VLLEHQKKVS
KTRHTRETVL RRAKRRWAPI PCSMQENSLG PFPLFLQQVE SDAAQNYTVF YSISGRGVDK
EPLNLFYIER DTGNLFCTRP VDREEYDVFD LIAYASTADG YSADLPLPLP IRVEDENDNH
PVFTEAIYNF EVLESSRPGT TVGVVCATDR DEPDTMHTRL KYSILQQTPR SPGLFSVHPS
TGVITTVSHY LDREVVDKYS LIMKVQDMDG QFFGLIGTST CIITVTDSND NAPTFRQNAY
EAFVEENAFN VEILRIPIED KDLINTANWR VNFTILKGNE NGHFKISTDK ETNEGVLSVV
KPLNYEENRQ VNLEIGVNNE APFARDIPRV TALNRALVTV HVRDLDEGPE CTPAAQYVRI
KENLAVGSKI NGYKAYDPEN RNGNGLRYKK LHDPKGWITI DEISGSIITS KILDREVETP
KNELYNITVL AIDKDDRSCT GTLAVNIEDV NDNPPEILQE YVVICKPKMG YTDILAVDPD
EPVHGAPFYF SLPNTSPEIS RLWSLTKVND TAARLSYQKN AGFQEYTIPI TVKDRAGQAA
TKLLRVNLCE CTHPTQCRAT SRSTGVILGK WAILAILLGI ALLFSVLLTL VCGVFGATKG
KRFPEDLAQQ NLIISNTEAP GDDRVCSANG FMTQTTNNSS QGFCGTMGSG MKNGGQETIE
MMKGGNQTLE SCRGAGHHHT LDSCRGGHTE VDNCRYTYSE WHSFTQPRLG EKLHRCNQNE
DRMPSQDYVL TYNYEGRGSP AGSVGCCSEK QEEDGLDFLN NLEPKFITLA EACTKR*
speed 0.86 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: 0.999994571946993 (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) chr18:28611061A>TN/A show variant in all transcripts   IGV
HGNC symbol DSC3
Ensembl transcript ID ENST00000434452
Genbank transcript ID NM_024423
UniProt peptide Q14574
alteration type single base exchange
alteration region CDS
DNA changes c.232T>A
cDNA.387T>A
g.11721T>A
AA changes S78T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 78
frameshift no
known variant Reference ID: rs276937
databasehomozygous (T/T)heterozygousallele carriers
1000G53711041641
ExAC100381269122729
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0610.099
1.1050.122
(flanking)-0.4650.124
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased11718wt: 0.61 / mu: 0.84wt: ATGATGGGTCAGTGT
mu: ATGATGGGACAGTGT		 GATG|ggtc
Donor gained117230.35mu: GGGACAGTGTACACA GACA|gtgt
distance from splice site 78
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      78SDPDFRVLNDGSVYTARAVALSDK
mutated  all conserved    78SDPDFRVLNDGTVYTARAVALSD
Ptroglodytes  all identical  ENSPTRG00000009940  78SDPDFRVLNDGSVYTARAVALSD
Mmulatta  all identical  ENSMMUG00000007668  78GDPDFRVLSDGSVYTARAVVLSD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000059898  78VLDDGSVYPTRAVVLSD
Ggallus  all identical  ENSGALG00000015140  55SDGSFKVLEDGSVYTTS
Trubripes  not conserved  ENSTRUG00000007388  92FAISGAGKIEVAAPMVVSP
Drerio  all identical  ENSDARG00000039677  114GSIVTLRSLVIST
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000004721  77LEDGSIFAQKRISLAG
protein features
start (aa)end (aa)featuredetails 
28135PROPEPPotential. /FTId=PRO_0000003875.lost
136243DOMAINCadherin 1.might get lost (downstream of altered splice site)
136690TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
166166CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
244355DOMAINCadherin 2.might get lost (downstream of altered splice site)
356471DOMAINCadherin 3.might get lost (downstream of altered splice site)
392392CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
472579DOMAINCadherin 4.might get lost (downstream of altered splice site)
546546CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
580690DOMAINCadherin 5.might get lost (downstream of altered splice site)
629629CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
691711TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
712896TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
818818MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
859859MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
863863MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
868868MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2520 / 2520
position (AA) of stopcodon in wt / mu AA sequence 840 / 840
position of stopcodon in wt / mu cDNA 2675 / 2675
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 156 / 156
chromosome 18
strand -1
last intron/exon boundary 2692
theoretical NMD boundary in CDS 2486
length of CDS 2520
coding sequence (CDS) position 232
cDNA position
(for ins/del: last normal base / first normal base)		 387
gDNA position
(for ins/del: last normal base / first normal base)		 11721
chromosomal position
(for ins/del: last normal base / first normal base)		 28611061
original gDNA sequence snippet TCAGAGTTCTAAATGATGGGTCAGTGTACACAGCCAGGGCT
altered gDNA sequence snippet TCAGAGTTCTAAATGATGGGACAGTGTACACAGCCAGGGCT
original cDNA sequence snippet TCAGAGTTCTAAATGATGGGTCAGTGTACACAGCCAGGGCT
altered cDNA sequence snippet TCAGAGTTCTAAATGATGGGACAGTGTACACAGCCAGGGCT
wildtype AA sequence MAAAGPRRSV RGAVCLHLLL TLVIFSRAGE ACKKVILNVP SKLEADKIIG RVNLEECFRS
ADLIRSSDPD FRVLNDGSVY TARAVALSDK KRSFTIWLSD KRKQTQKEVT VLLEHQKKVS
KTRHTRETVL RRAKRRWAPI PCSMQENSLG PFPLFLQQVE SDAAQNYTVF YSISGRGVDK
EPLNLFYIER DTGNLFCTRP VDREEYDVFD LIAYASTADG YSADLPLPLP IRVEDENDNH
PVFTEAIYNF EVLESSRPGT TVGVVCATDR DEPDTMHTRL KYSILQQTPR SPGLFSVHPS
TGVITTVSHY LDREVVDKYS LIMKVQDMDG QFFGLIGTST CIITVTDSND NAPTFRQNAY
EAFVEENAFN VEILRIPIED KDLINTANWR VNFTILKGNE NGHFKISTDK ETNEGVLSVV
KPLNYEENRQ VNLEIGVNNE APFARDIPRV TALNRALVTV HVRDLDEGPE CTPAAQYVRI
KENLAVGSKI NGYKAYDPEN RNGNGLRYKK LHDPKGWITI DEISGSIITS KILDREVETP
KNELYNITVL AIDKDDRSCT GTLAVNIEDV NDNPPEILQE YVVICKPKMG YTDILAVDPD
EPVHGAPFYF SLPNTSPEIS RLWSLTKVND TAARLSYQKN AGFQEYTIPI TVKDRAGQAA
TKLLRVNLCE CTHPTQCRAT SRSTGVILGK WAILAILLGI ALLFSVLLTL VCGVFGATKG
KRFPEDLAQQ NLIISNTEAP GDDRVCSANG FMTQTTNNSS QGFCGTMGSG MKNGGQETIE
MMKGGNQTLE SCRGAGHHHT LDSCRGGHTE VDNCRYTYSE WHSFTQPRLG EESIRGHTG*
mutated AA sequence MAAAGPRRSV RGAVCLHLLL TLVIFSRAGE ACKKVILNVP SKLEADKIIG RVNLEECFRS
ADLIRSSDPD FRVLNDGTVY TARAVALSDK KRSFTIWLSD KRKQTQKEVT VLLEHQKKVS
KTRHTRETVL RRAKRRWAPI PCSMQENSLG PFPLFLQQVE SDAAQNYTVF YSISGRGVDK
EPLNLFYIER DTGNLFCTRP VDREEYDVFD LIAYASTADG YSADLPLPLP IRVEDENDNH
PVFTEAIYNF EVLESSRPGT TVGVVCATDR DEPDTMHTRL KYSILQQTPR SPGLFSVHPS
TGVITTVSHY LDREVVDKYS LIMKVQDMDG QFFGLIGTST CIITVTDSND NAPTFRQNAY
EAFVEENAFN VEILRIPIED KDLINTANWR VNFTILKGNE NGHFKISTDK ETNEGVLSVV
KPLNYEENRQ VNLEIGVNNE APFARDIPRV TALNRALVTV HVRDLDEGPE CTPAAQYVRI
KENLAVGSKI NGYKAYDPEN RNGNGLRYKK LHDPKGWITI DEISGSIITS KILDREVETP
KNELYNITVL AIDKDDRSCT GTLAVNIEDV NDNPPEILQE YVVICKPKMG YTDILAVDPD
EPVHGAPFYF SLPNTSPEIS RLWSLTKVND TAARLSYQKN AGFQEYTIPI TVKDRAGQAA
TKLLRVNLCE CTHPTQCRAT SRSTGVILGK WAILAILLGI ALLFSVLLTL VCGVFGATKG
KRFPEDLAQQ NLIISNTEAP GDDRVCSANG FMTQTTNNSS QGFCGTMGSG MKNGGQETIE
MMKGGNQTLE SCRGAGHHHT LDSCRGGHTE VDNCRYTYSE WHSFTQPRLG EESIRGHTG*
speed 0.43 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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