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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000222214
Querying Taster for transcript #2: ENST00000591470
Querying Taster for transcript #3: ENST00000457854
Querying Taster for transcript #4: ENST00000422947
Querying Taster for transcript #5: ENST00000293695
MT speed 0 s - this script 4.22744 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GCDHdisease_causing_automatic0.999999999782745simple_aae0T372Isingle base exchangers121434368show file
GCDHdisease_causing_automatic0.999999999865279simple_aae0T416Isingle base exchangers121434368show file
GCDHdisease_causing_automatic0.999999999865279simple_aae0T416Isingle base exchangers121434368show file
GCDHdisease_causing_automatic1without_aae0single base exchangers121434368show file
SYCE2disease_causing_automatic1without_aae0single base exchangers121434368show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999782745 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960721)
  • known disease mutation: rs2084 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13010285C>TN/A show variant in all transcripts   IGV
HGNC symbol GCDH
Ensembl transcript ID ENST00000422947
Genbank transcript ID N/A
UniProt peptide Q92947
alteration type single base exchange
alteration region CDS
DNA changes c.1115C>T
cDNA.1373C>T
g.8446C>T
AA changes T372I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 372
frameshift no
known variant Reference ID: rs121434368
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2084 (pathogenic for Glutaric aciduria, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6291
5.6051
(flanking)-0.5650.864
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 increased8450wt: 0.2395 / mu: 0.2405 (marginal change - not scored)wt: ACACATGACATTCAC
mu: ATACATGACATTCAC		 ACAT|gaca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      372MNLEAVNTYEGTHDIHALILGRAI
mutated  not conserved    372MNLEAVNTYEGIHDIHALILGRA
Ptroglodytes  all identical  ENSPTRG00000010548  416VNTYEGTHDIHALILGRA
Mmulatta  all identical  ENSMMUG00000007043  416VNTYEGTHDIHALILGRA
Fcatus  all identical  ENSFCAG00000000477  416YEGTHDIHALILGRA
Mmusculus  all identical  ENSMUSG00000003809  416VNTYEGTHDIHALILGRA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  422LEAVNTYEGTHDIHALILGRA
Drerio  not conserved  ENSDARG00000038361  386VNTYEGQRE
Dmelanogaster  all identical  FBgn0031824  399ESVNTYEGTHDIHALILGRA
Celegans  all identical  F54D5.7  390VNLETVNTYEGTHDVHAL
Xtropicalis  all identical  ENSXETG00000007932  418VNTYEGTHDVHALILGRA
protein features
start (aa)end (aa)featuredetails 
364388HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1185 / 1185
position (AA) of stopcodon in wt / mu AA sequence 395 / 395
position of stopcodon in wt / mu cDNA 1443 / 1443
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 259 / 259
chromosome 19
strand 1
last intron/exon boundary 1370
theoretical NMD boundary in CDS 1061
length of CDS 1185
coding sequence (CDS) position 1115
cDNA position
(for ins/del: last normal base / first normal base)		 1373
gDNA position
(for ins/del: last normal base / first normal base)		 8446
chromosomal position
(for ins/del: last normal base / first normal base)		 13010285
original gDNA sequence snippet GTATTAATCTTGTCCAGGTACACATGACATTCACGCCCTGA
altered gDNA sequence snippet GTATTAATCTTGTCCAGGTATACATGACATTCACGCCCTGA
original cDNA sequence snippet CGTGAACACCTACGAAGGTACACATGACATTCACGCCCTGA
altered cDNA sequence snippet CGTGAACACCTACGAAGGTATACATGACATTCACGCCCTGA
wildtype AA sequence MRSSSGTPSA PTARRDSCLA SCWPIATKSL ALLPRLECSG TILAHCKFCL PGSSDSPAST
PLVAGITGYG CAGVSSVAYG LLARELERVD SGYRSAMSVQ SSLVMHPIYA YGSEEQRQKY
LPQLAKGELL GCFGLTEPNS GSDPSSMETR AHYNSSNKSY TLNGTKTWIT NSPMADLFVV
WARCEDGCIR GFLLEKGMRG LSAPRIQGKF SLRASATGMI IMDGVEVPEE NVLPGASSLG
GPFGCLNNAR YGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP EMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIRHA
MNLEAVNTYE GTHDIHALIL GRAITGIQAF TASK*
mutated AA sequence MRSSSGTPSA PTARRDSCLA SCWPIATKSL ALLPRLECSG TILAHCKFCL PGSSDSPAST
PLVAGITGYG CAGVSSVAYG LLARELERVD SGYRSAMSVQ SSLVMHPIYA YGSEEQRQKY
LPQLAKGELL GCFGLTEPNS GSDPSSMETR AHYNSSNKSY TLNGTKTWIT NSPMADLFVV
WARCEDGCIR GFLLEKGMRG LSAPRIQGKF SLRASATGMI IMDGVEVPEE NVLPGASSLG
GPFGCLNNAR YGIAWGVLGA SEFCLHTARQ YALDRMQFGV PLARNQLIQK KLADMLTEIT
LGLHACLQLG RLKDQDKAAP EMVSLLKRNN CGKALDIARQ ARDMLGGNGI SDEYHVIRHA
MNLEAVNTYE GIHDIHALIL GRAITGIQAF TASK*
speed 0.89 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: 0.999999999865279 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960721)
  • known disease mutation: rs2084 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13010285C>TN/A show variant in all transcripts   IGV
HGNC symbol GCDH
Ensembl transcript ID ENST00000222214
Genbank transcript ID NM_000159
UniProt peptide Q92947
alteration type single base exchange
alteration region CDS
DNA changes c.1247C>T
cDNA.1458C>T
g.8446C>T
AA changes T416I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 416
frameshift no
known variant Reference ID: rs121434368
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2084 (pathogenic for Glutaric aciduria, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6291
5.6051
(flanking)-0.5650.864
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 increased8450wt: 0.2395 / mu: 0.2405 (marginal change - not scored)wt: ACACATGACATTCAC
mu: ATACATGACATTCAC		 ACAT|gaca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      416MNLEAVNTYEGTHDIHALILGRAI
mutated  not conserved    416MNLEAVNTYEGIHDIH
Ptroglodytes  all identical  ENSPTRG00000010548  416MNLEAVNTYEGTHDIH
Mmulatta  all identical  ENSMMUG00000007043  416MNLEAVNTYEGTHDIH
Fcatus  all identical  ENSFCAG00000000477  416MNLESVNTYEGTHDIH
Mmusculus  all identical  ENSMUSG00000003809  416MNLEAVNTYEGTHDIHALILGRA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  422GTHDIHALILGRA
Drerio  not conserved  ENSDARG00000038361  386LNLEAVNTYEGQRE
Dmelanogaster  all identical  FBgn0031824  399INLESVNTYEGTHDIHALILGRA
Celegans  all identical  F54D5.7  390ETVNTYEGTHDVHALILGRA
Xtropicalis  all identical  ENSXETG00000007932  418MNLESVNTYEGTHDVHALILGRA
protein features
start (aa)end (aa)featuredetails 
416418NP_BINDFAD.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1317 / 1317
position (AA) of stopcodon in wt / mu AA sequence 439 / 439
position of stopcodon in wt / mu cDNA 1528 / 1528
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 212 / 212
chromosome 19
strand 1
last intron/exon boundary 1455
theoretical NMD boundary in CDS 1193
length of CDS 1317
coding sequence (CDS) position 1247
cDNA position
(for ins/del: last normal base / first normal base)		 1458
gDNA position
(for ins/del: last normal base / first normal base)		 8446
chromosomal position
(for ins/del: last normal base / first normal base)		 13010285
original gDNA sequence snippet GTATTAATCTTGTCCAGGTACACATGACATTCACGCCCTGA
altered gDNA sequence snippet GTATTAATCTTGTCCAGGTATACATGACATTCACGCCCTGA
original cDNA sequence snippet CGTGAACACCTACGAAGGTACACATGACATTCACGCCCTGA
altered cDNA sequence snippet CGTGAACACCTACGAAGGTATACATGACATTCACGCCCTGA
wildtype AA sequence MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL
TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS
VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT
EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEGTHDIH
ALILGRAITG IQAFTASK*
mutated AA sequence MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL
TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS
VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT
EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEGIHDIH
ALILGRAITG IQAFTASK*
speed 0.78 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: 0.999999999865279 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960721)
  • known disease mutation: rs2084 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13010285C>TN/A show variant in all transcripts   IGV
HGNC symbol GCDH
Ensembl transcript ID ENST00000591470
Genbank transcript ID N/A
UniProt peptide Q92947
alteration type single base exchange
alteration region CDS
DNA changes c.1247C>T
cDNA.1392C>T
g.8446C>T
AA changes T416I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 416
frameshift no
known variant Reference ID: rs121434368
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2084 (pathogenic for Glutaric aciduria, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6291
5.6051
(flanking)-0.5650.864
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 increased8450wt: 0.2395 / mu: 0.2405 (marginal change - not scored)wt: ACACATGACATTCAC
mu: ATACATGACATTCAC		 ACAT|gaca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      416MNLEAVNTYEGTHDIHALILGRAI
mutated  not conserved    416MNLEAVNTYEGIHDIH
Ptroglodytes  all identical  ENSPTRG00000010548  416MNLEAVNTYEGTHDIH
Mmulatta  all identical  ENSMMUG00000007043  416MNLEAVNTYEGTHDIH
Fcatus  all identical  ENSFCAG00000000477  416MNLESVNTYEGTHDIH
Mmusculus  all identical  ENSMUSG00000003809  416MNLEAVNTYEGTHDIHALILGRA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008257  422GTHDIHALILGRA
Drerio  not conserved  ENSDARG00000038361  386LNLEAVNTYEGQRE
Dmelanogaster  all identical  FBgn0031824  399INLESVNTYEGTHDIHALILGRA
Celegans  all identical  F54D5.7  390ETVNTYEGTHDVHALILGRA
Xtropicalis  all identical  ENSXETG00000007932  418MNLESVNTYEGTHDVHALILGRA
protein features
start (aa)end (aa)featuredetails 
416418NP_BINDFAD.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1317 / 1317
position (AA) of stopcodon in wt / mu AA sequence 439 / 439
position of stopcodon in wt / mu cDNA 1462 / 1462
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 146 / 146
chromosome 19
strand 1
last intron/exon boundary 1389
theoretical NMD boundary in CDS 1193
length of CDS 1317
coding sequence (CDS) position 1247
cDNA position
(for ins/del: last normal base / first normal base)		 1392
gDNA position
(for ins/del: last normal base / first normal base)		 8446
chromosomal position
(for ins/del: last normal base / first normal base)		 13010285
original gDNA sequence snippet GTATTAATCTTGTCCAGGTACACATGACATTCACGCCCTGA
altered gDNA sequence snippet GTATTAATCTTGTCCAGGTATACATGACATTCACGCCCTGA
original cDNA sequence snippet CGTGAACACCTACGAAGGTACACATGACATTCACGCCCTGA
altered cDNA sequence snippet CGTGAACACCTACGAAGGTATACATGACATTCACGCCCTGA
wildtype AA sequence MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL
TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS
VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT
EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEGTHDIH
ALILGRAITG IQAFTASK*
mutated AA sequence MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL
TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS
VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT
EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEGIHDIH
ALILGRAITG IQAFTASK*
speed 0.60 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: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM960721)
  • known disease mutation: rs2084 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13010285C>TN/A show variant in all transcripts   IGV
HGNC symbol GCDH
Ensembl transcript ID ENST00000457854
Genbank transcript ID NM_013976
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.8446C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121434368
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2084 (pathogenic for Glutaric aciduria, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6291
5.6051
(flanking)-0.5650.864
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased8442wt: 0.9038 / mu: 0.9201 (marginal change - not scored)wt: CTCTGTATTAATCTTGTCCAGGTACACATGACATTCACGCC
mu: CTCTGTATTAATCTTGTCCAGGTATACATGACATTCACGCC		 ccag|GTAC
Donor marginally increased8450wt: 0.2395 / mu: 0.2405 (marginal change - not scored)wt: ACACATGACATTCAC
mu: ATACATGACATTCAC		 ACAT|gaca
distance from splice site 229
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 78 / 78
chromosome 19
strand 1
last intron/exon boundary 1321
theoretical NMD boundary in CDS 1193
length of CDS 1287
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)		 8446
chromosomal position
(for ins/del: last normal base / first normal base)		 13010285
original gDNA sequence snippet GTATTAATCTTGTCCAGGTACACATGACATTCACGCCCTGA
altered gDNA sequence snippet GTATTAATCTTGTCCAGGTATACATGACATTCACGCCCTGA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MALRGVSVRL LSRGPGLHVL RTWVSSAAQT EKGGRTQSQL AKSSRPEFDW QDPLVLEEQL
TTDEILIRDT FRTYCQERLM PRILLANRNE VFHREIISEM GELGVLGPTI KGYGCAGVSS
VAYGLLAREL ERVDSGYRSA MSVQSSLVMH PIYAYGSEEQ RQKYLPQLAK GELLGCFGLT
EPNSGSDPSS METRAHYNSS NKSYTLNGTK TWITNSPMAD LFVVWARCED GCIRGFLLEK
GMRGLSAPRI QGKFSLRASA TGMIIMDGVE VPEENVLPGA SSLGGPFGCL NNARYGIAWG
VLGASEFCLH TARQYALDRM QFGVPLARNQ LIQKKLADML TEITLGLHAC LQLGRLKDQD
KAAPEMVSLL KRNNCGKALD IARQARDMLG GNGISDEYHV IRHAMNLEAV NTYEVVQMCS
LKRRWNSL*
mutated AA sequence N/A
speed 0.57 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: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM960721)
  • known disease mutation: rs2084 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:13010285C>TN/A show variant in all transcripts   IGV
HGNC symbol SYCE2
Ensembl transcript ID ENST00000293695
Genbank transcript ID NM_001105578
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.19806G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121434368
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2084 (pathogenic for Glutaric aciduria, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960721)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6291
5.6051
(flanking)-0.5650.864
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 increased19798wt: 0.9889 / mu: 0.9906 (marginal change - not scored)wt: GTGAATGTCATGTGT
mu: GTGAATGTCATGTAT		 GAAT|gtca
distance from splice site 86
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 20 / 20
chromosome 19
strand -1
last intron/exon boundary 632
theoretical NMD boundary in CDS 562
length of CDS 657
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)		 19806
chromosomal position
(for ins/del: last normal base / first normal base)		 13010285
original gDNA sequence snippet TCAGGGCGTGAATGTCATGTGTACCTGGACAAGATTAATAC
altered gDNA sequence snippet TCAGGGCGTGAATGTCATGTATACCTGGACAAGATTAATAC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MERQGVDVPH VKCKDQEPQP LGESKEHPRW EENCEEEAGG GPASASCQLT VLEGKSGLYF
SSLDSSIDIL QKRAQELIEN INKSRQKDHA LMTNFRNSLK TKVSDLTEKL EERIYQIYND
HNKIIQEKLQ EFTQKMAKIS HLETELKQVC HSVETVYKDL CLQPEQSLRL RWGPDHSRGK
SPPRPGNSQP PDVFVSSVAE TTSQATASEV QTNRDGEC*
mutated AA sequence N/A
speed 0.59 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
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Problems