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 6 transcript(s)...
Querying Taster for transcript #1: ENST00000300853
Querying Taster for transcript #2: ENST00000423698
Querying Taster for transcript #3: ENST00000340192
Querying Taster for transcript #4: ENST00000591636
Querying Taster for transcript #5: ENST00000589165
Querying Taster for transcript #6: ENST00000013807
MT speed 0 s - this script 5.568665 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ERCC1disease_causing_automatic0.204434405916677simple_aaeaffected0F231Lsingle base exchangers121913028show file
ERCC1disease_causing_automatic0.204434405916677simple_aaeaffected0F231Lsingle base exchangers121913028show file
ERCC1disease_causing_automatic0.204434405916677simple_aaeaffected0F231Lsingle base exchangers121913028show file
ERCC1disease_causing_automatic0.610301788013797simple_aaeaffected0F159Lsingle base exchangers121913028show file
ERCC1disease_causing_automatic0.686980696755333simple_aaeaffected0F231Lsingle base exchangers121913028show file
ERCC1disease_causing_automatic0.9999999996391without_aae0single base exchangers121913028show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.204434405916677 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070925)
  • known disease mutation: rs16778 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45918128G>CN/A show variant in all transcripts   IGV
HGNC symbol ERCC1
Ensembl transcript ID ENST00000300853
Genbank transcript ID NM_001983
UniProt peptide P07992
alteration type single base exchange
alteration region CDS
DNA changes c.693C>G
cDNA.1285C>G
g.63959C>G
AA changes F231L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 231
frameshift no
known variant Reference ID: rs121913028
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs16778 (pathogenic for Cerebrooculofacioskeletal syndrome 4|Cockayne syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1690.995
0.4360.997
(flanking)2.4031
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc lost639680.39wt: GAGCAGGACTTCGTCTCCCGGGTGAGGCCACCTCACCTCCC ccgg|GTGA
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      231ADLLMEKLEQDFVSRVTECLTTVK
mutated  not conserved    231ADLLMEKLEQDLVSRVTECLT
Ptroglodytes  all identical  ENSPTRG00000011152  231ADLLMEKLEQDFVSRVTECLT
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000003549  231ADLLMEKLEQNFLSRATECLT
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013151  269ADTLKEQVEKDYLSKVTECLTTV
Drerio  all conserved  ENSDARG00000031680  272ADLLKEQVEKNYLSQVTDCLTTV
Dmelanogaster  not conserved  FBgn0028434  194PDLIMERVESNPHQKLLAALTNI
Celegans  not conserved  F10G8.7  183ITIKKKAIDDGGDSSMSDERRRNREAAIGFLTAA
Xtropicalis  not conserved  ENSXETG00000026094  197ADVLKERTEKDLMSRMAECLTTV
protein features
start (aa)end (aa)featuredetails 
242244STRANDmight get lost (downstream of altered splice site)
247257HELIXmight get lost (downstream of altered splice site)
260264HELIXmight get lost (downstream of altered splice site)
268272HELIXmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
280290HELIXmight get lost (downstream of altered splice site)
293295STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 894 / 894
position (AA) of stopcodon in wt / mu AA sequence 298 / 298
position of stopcodon in wt / mu cDNA 1486 / 1486
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 593 / 593
chromosome 19
strand -1
last intron/exon boundary 1436
theoretical NMD boundary in CDS 793
length of CDS 894
coding sequence (CDS) position 693
cDNA position
(for ins/del: last normal base / first normal base)		 1285
gDNA position
(for ins/del: last normal base / first normal base)		 63959
chromosomal position
(for ins/del: last normal base / first normal base)		 45918128
original gDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGAGGCCACC
altered gDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGAGGCCACC
original cDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGACTGAATG
altered cDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGACTGAATG
wildtype AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW SPEEAGRYLE TYKAYEQKPA DLLMEKLEQD FVSRVTECLT
TVKSVNKTDS QTLLTTFGSL EQLIAASRED LALCPGLGPQ KARRLFDVLH EPFLKVP*
mutated AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW SPEEAGRYLE TYKAYEQKPA DLLMEKLEQD LVSRVTECLT
TVKSVNKTDS QTLLTTFGSL EQLIAASRED LALCPGLGPQ KARRLFDVLH EPFLKVP*
speed 1.31 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

disease causing

 Model: simple_aae, prob: 0.204434405916677 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070925)
  • known disease mutation: rs16778 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45918128G>CN/A show variant in all transcripts   IGV
HGNC symbol ERCC1
Ensembl transcript ID ENST00000589165
Genbank transcript ID N/A
UniProt peptide P07992
alteration type single base exchange
alteration region CDS
DNA changes c.693C>G
cDNA.1245C>G
g.63959C>G
AA changes F231L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 231
frameshift no
known variant Reference ID: rs121913028
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs16778 (pathogenic for Cerebrooculofacioskeletal syndrome 4|Cockayne syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1690.995
0.4360.997
(flanking)2.4031
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc lost639680.39wt: GAGCAGGACTTCGTCTCCCGGGTGAGGCCACCTCACCTCCC ccgg|GTGA
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      231ADLLMEKLEQDFVSRVTECLTTVK
mutated  not conserved    231ADLLMEKLEQDLVSRVTECLT
Ptroglodytes  all identical  ENSPTRG00000011152  231ADLLMEKLEQDFVSRVTECLT
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000003549  231ADLLMEKLEQNFLSRATECLT
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013151  269ADTLKEQVEKDYLSKVTECLTTV
Drerio  all conserved  ENSDARG00000031680  272ADLLKEQVEKNYLSQVTDCLTTV
Dmelanogaster  not conserved  FBgn0028434  194PDLIMERVESNPHQKLLAALTNI
Celegans  not conserved  F10G8.7  183ITIKKKAIDDGGDSSMSDERRRNREAAIGFLTAA
Xtropicalis  not conserved  ENSXETG00000026094  197ADVLKERTEKDLMSRMAECLTTV
protein features
start (aa)end (aa)featuredetails 
242244STRANDmight get lost (downstream of altered splice site)
247257HELIXmight get lost (downstream of altered splice site)
260264HELIXmight get lost (downstream of altered splice site)
268272HELIXmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
280290HELIXmight get lost (downstream of altered splice site)
293295STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 894 / 894
position (AA) of stopcodon in wt / mu AA sequence 298 / 298
position of stopcodon in wt / mu cDNA 1446 / 1446
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 553 / 553
chromosome 19
strand -1
last intron/exon boundary 1396
theoretical NMD boundary in CDS 793
length of CDS 894
coding sequence (CDS) position 693
cDNA position
(for ins/del: last normal base / first normal base)		 1245
gDNA position
(for ins/del: last normal base / first normal base)		 63959
chromosomal position
(for ins/del: last normal base / first normal base)		 45918128
original gDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGAGGCCACC
altered gDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGAGGCCACC
original cDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGACTGAATG
altered cDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGACTGAATG
wildtype AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW SPEEAGRYLE TYKAYEQKPA DLLMEKLEQD FVSRVTECLT
TVKSVNKTDS QTLLTTFGSL EQLIAASRED LALCPGLGPQ KARRLFDVLH EPFLKVP*
mutated AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW SPEEAGRYLE TYKAYEQKPA DLLMEKLEQD LVSRVTECLT
TVKSVNKTDS QTLLTTFGSL EQLIAASRED LALCPGLGPQ KARRLFDVLH EPFLKVP*
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

disease causing

 Model: simple_aae, prob: 0.204434405916677 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070925)
  • known disease mutation: rs16778 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45918128G>CN/A show variant in all transcripts   IGV
HGNC symbol ERCC1
Ensembl transcript ID ENST00000013807
Genbank transcript ID NM_202001
UniProt peptide P07992
alteration type single base exchange
alteration region CDS
DNA changes c.693C>G
cDNA.885C>G
g.63959C>G
AA changes F231L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 231
frameshift no
known variant Reference ID: rs121913028
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs16778 (pathogenic for Cerebrooculofacioskeletal syndrome 4|Cockayne syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1690.995
0.4360.997
(flanking)2.4031
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc lost639680.39wt: GAGCAGGACTTCGTCTCCCGGGTGAGGCCACCTCACCTCCC ccgg|GTGA
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      231ADLLMEKLEQDFVSRVTECLTTVK
mutated  not conserved    231ADLLMEKLEQDLVSRVTECLT
Ptroglodytes  all identical  ENSPTRG00000011152  231ADLLMEKLEQDFVSRVTECLT
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000003549  231ADLLMEKLEQNFLSRATECLT
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013151  269ADTLKEQVEKDYLSKVTECLTTV
Drerio  all conserved  ENSDARG00000031680  272ADLLKEQVEKNYLSQVTDCLTTV
Dmelanogaster  not conserved  FBgn0028434  194PDLIMERVESNPHQKLLAALTNI
Celegans  not conserved  F10G8.7  183ITIKKKAIDDGGDSSMSDERRRNREAAIGFLTAA
Xtropicalis  not conserved  ENSXETG00000026094  197ADVLKERTEKDLMSRMAECLTTV
protein features
start (aa)end (aa)featuredetails 
242244STRANDmight get lost (downstream of altered splice site)
247257HELIXmight get lost (downstream of altered splice site)
260264HELIXmight get lost (downstream of altered splice site)
268272HELIXmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
280290HELIXmight get lost (downstream of altered splice site)
293295STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 972 / 972
position (AA) of stopcodon in wt / mu AA sequence 324 / 324
position of stopcodon in wt / mu cDNA 1164 / 1164
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 193 / 193
chromosome 19
strand -1
last intron/exon boundary 967
theoretical NMD boundary in CDS 724
length of CDS 972
coding sequence (CDS) position 693
cDNA position
(for ins/del: last normal base / first normal base)		 885
gDNA position
(for ins/del: last normal base / first normal base)		 63959
chromosomal position
(for ins/del: last normal base / first normal base)		 45918128
original gDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGAGGCCACC
altered gDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGAGGCCACC
original cDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGACTGAATG
altered cDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGACTGAATG
wildtype AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW SPEEAGRYLE TYKAYEQKPA DLLMEKLEQD FVSRVTECLT
TVKSVNKTDS QTLLTTFGSL EQLIAASRED LALCPGLGPQ KVRALGKNPR SWGKERAPNK
HNLRPQSFKV KKEPKTRHSG FRL*
mutated AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW SPEEAGRYLE TYKAYEQKPA DLLMEKLEQD LVSRVTECLT
TVKSVNKTDS QTLLTTFGSL EQLIAASRED LALCPGLGPQ KVRALGKNPR SWGKERAPNK
HNLRPQSFKV KKEPKTRHSG FRL*
speed 1.36 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

disease causing

 Model: simple_aae, prob: 0.610301788013797 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070925)
  • known disease mutation: rs16778 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45918128G>CN/A show variant in all transcripts   IGV
HGNC symbol ERCC1
Ensembl transcript ID ENST00000423698
Genbank transcript ID N/A
UniProt peptide P07992
alteration type single base exchange
alteration region CDS
DNA changes c.477C>G
cDNA.577C>G
g.63959C>G
AA changes F159L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 159
frameshift no
known variant Reference ID: rs121913028
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs16778 (pathogenic for Cerebrooculofacioskeletal syndrome 4|Cockayne syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1690.995
0.4360.997
(flanking)2.4031
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc lost639680.39wt: GAGCAGGACTTCGTCTCCCGGGTGAGGCCACCTCACCTCCC ccgg|GTGA
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      159ADLLMEKLEQDFVSRVTECLTTVK
mutated  not conserved    159ADLLMEKLEQDLVSRVTECLTTV
Ptroglodytes  all identical  ENSPTRG00000011152  231LMEKLEQDFVSRVTECLTTV
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000003549  231LMEKLEQNFLSRATECLTTV
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013151  269LKEQVEKDYLSKVTECLTTV
Drerio  all conserved  ENSDARG00000031680  272LKEQVEKNYLSQVTDCLTTV
Dmelanogaster  not conserved  FBgn0028434  194PDLIMERVESNPHQKLLAALTNI
Celegans  not conserved  F10G8.7  183DDGGDSSMSDERRRNREAAIGFLTAA
Xtropicalis  not conserved  ENSXETG00000026094  197EKDLMSRMAECLTTV
protein features
start (aa)end (aa)featuredetails 
152160HELIXlost
163172STRANDmight get lost (downstream of altered splice site)
175177STRANDmight get lost (downstream of altered splice site)
179192HELIXmight get lost (downstream of altered splice site)
195201STRANDmight get lost (downstream of altered splice site)
202213HELIXmight get lost (downstream of altered splice site)
222226HELIXmight get lost (downstream of altered splice site)
242244STRANDmight get lost (downstream of altered splice site)
247257HELIXmight get lost (downstream of altered splice site)
260264HELIXmight get lost (downstream of altered splice site)
268272HELIXmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
280290HELIXmight get lost (downstream of altered splice site)
293295STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 678 / 678
position (AA) of stopcodon in wt / mu AA sequence 226 / 226
position of stopcodon in wt / mu cDNA 778 / 778
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 101 / 101
chromosome 19
strand -1
last intron/exon boundary 728
theoretical NMD boundary in CDS 577
length of CDS 678
coding sequence (CDS) position 477
cDNA position
(for ins/del: last normal base / first normal base)		 577
gDNA position
(for ins/del: last normal base / first normal base)		 63959
chromosomal position
(for ins/del: last normal base / first normal base)		 45918128
original gDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGAGGCCACC
altered gDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGAGGCCACC
original cDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGACTGAATG
altered cDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGACTGAATG
wildtype AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVRGNPV LKFVRNVPWE FGDVIPDYVL
GQSTCALFLS LRYHNLHPDY IHGRLQSLGK NFALRVLLVQ VDVKDPQQAL KELAKMCILA
DCTLILAWSP EEAGRYLETY KAYEQKPADL LMEKLEQDFV SRVTECLTTV KSVNKTDSQT
LLTTFGSLEQ LIAASREDLA LCPGLGPQKA RRLFDVLHEP FLKVP*
mutated AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVRGNPV LKFVRNVPWE FGDVIPDYVL
GQSTCALFLS LRYHNLHPDY IHGRLQSLGK NFALRVLLVQ VDVKDPQQAL KELAKMCILA
DCTLILAWSP EEAGRYLETY KAYEQKPADL LMEKLEQDLV SRVTECLTTV KSVNKTDSQT
LLTTFGSLEQ LIAASREDLA LCPGLGPQKA RRLFDVLHEP FLKVP*
speed 0.47 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

disease causing

 Model: simple_aae, prob: 0.686980696755333 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070925)
  • known disease mutation: rs16778 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45918128G>CN/A show variant in all transcripts   IGV
HGNC symbol ERCC1
Ensembl transcript ID ENST00000340192
Genbank transcript ID NM_001166049
UniProt peptide P07992
alteration type single base exchange
alteration region CDS
DNA changes c.693C>G
cDNA.759C>G
g.63959C>G
AA changes F231L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 231
frameshift no
known variant Reference ID: rs121913028
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs16778 (pathogenic for Cerebrooculofacioskeletal syndrome 4|Cockayne syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1690.995
0.4360.997
(flanking)2.4031
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc lost639680.39wt: GAGCAGGACTTCGTCTCCCGGGTGAGGCCACCTCACCTCCC ccgg|GTGA
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      231ADLLMEKLEQDFVSRSLEQLIAAS
mutated  not conserved    231ADLLMEKLEQDLVSRSLEQLI
Ptroglodytes  all identical  ENSPTRG00000011152  231ADLLMEKLEQDFVSRVTECLT
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000003549  231ADLLMEKLEQNFLSRATECLT
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013151  269ADTLKEQVEKDYLSKVTECLTTVKSINKTDAITLLSTFSSVEGIMNA
Drerio  all conserved  ENSDARG00000031680  272ADLLKEQVEKNYLSQVTDCLTTVKSVNKTDAMTLLSTFSSLEGIIKA
Dmelanogaster  not conserved  FBgn0028434  195HQKLLAALTNIKPVNKTDAAALLHTFGNLGNIINA
Celegans  all identical  F10G8.7  183ITIKKKAIDDGGDSSMSDERRRNREAAIGFLTAARSITKTDADRLLFHFGTLQA
Xtropicalis  not conserved  ENSXETG00000026094  197ADVLKERTEKDLMSRMAECLTTVKYVNKTDSCTLFTTFGTLFDLAN
protein features
start (aa)end (aa)featuredetails 
242244STRANDmight get lost (downstream of altered splice site)
247257HELIXmight get lost (downstream of altered splice site)
260264HELIXmight get lost (downstream of altered splice site)
268272HELIXmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
280290HELIXmight get lost (downstream of altered splice site)
293295STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 822 / 822
position (AA) of stopcodon in wt / mu AA sequence 274 / 274
position of stopcodon in wt / mu cDNA 888 / 888
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 67 / 67
chromosome 19
strand -1
last intron/exon boundary 838
theoretical NMD boundary in CDS 721
length of CDS 822
coding sequence (CDS) position 693
cDNA position
(for ins/del: last normal base / first normal base)		 759
gDNA position
(for ins/del: last normal base / first normal base)		 63959
chromosomal position
(for ins/del: last normal base / first normal base)		 45918128
original gDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGAGGCCACC
altered gDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGAGGCCACC
original cDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGTCTCTGGAACA
altered cDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGTCTCTGGAACA
wildtype AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW SPEEAGRYLE TYKAYEQKPA DLLMEKLEQD FVSRSLEQLI
AASREDLALC PGLGPQKARR LFDVLHEPFL KVP*
mutated AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW SPEEAGRYLE TYKAYEQKPA DLLMEKLEQD LVSRSLEQLI
AASREDLALC PGLGPQKARR LFDVLHEPFL KVP*
speed 0.88 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

disease causing

 Model: without_aae, prob: 0.9999999996391 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM070925)
  • known disease mutation: rs16778 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45918128G>CN/A show variant in all transcripts   IGV
HGNC symbol ERCC1
Ensembl transcript ID ENST00000591636
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.63959C>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121913028
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs16778 (pathogenic for Cerebrooculofacioskeletal syndrome 4|Cockayne syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1690.995
0.4360.997
(flanking)2.4031
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 1951
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 128 / 128
chromosome 19
strand -1
last intron/exon boundary 730
theoretical NMD boundary in CDS 552
length of CDS 642
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)		 63959
chromosomal position
(for ins/del: last normal base / first normal base)		 45918128
original gDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGAGGCCACC
altered gDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGAGGCCACC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY
AEYAISQPLE GAGATCPTGS EPLAGETPNQ ALKPGAKSNS IIVSPRQRGN PVLKFVRNVP
WEFGDVIPDY VLGQSTCALF LSLRYHNLHP DYIHGRLQSL GKNFALRVLL VQVDVKDPQQ
ALKELAKMCI LADCTLILAW RPGGCLMSCT SPS*
mutated AA sequence N/A
speed 0.74 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