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: ENST00000432161
Querying Taster for transcript #2: ENST00000411726
Querying Taster for transcript #3: ENST00000242375
MT speed 2.99 s - this script 4.058661 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AKR1D1disease_causing_automatic0.999994136377947simple_aae0L106Fsingle base exchangers121918343show file
AKR1D1disease_causing_automatic0.999994136377947simple_aae0L106Fsingle base exchangers121918343show file
AKR1D1disease_causing_automatic0.999994136377947simple_aae0L106Fsingle base exchangers121918343show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999994136377947 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032542)
  • known disease mutation: rs5376 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:137776568C>TN/A show variant in all transcripts   IGV
HGNC symbol AKR1D1
Ensembl transcript ID ENST00000432161
Genbank transcript ID NM_001190907
UniProt peptide P51857
alteration type single base exchange
alteration region CDS
DNA changes c.316C>T
cDNA.403C>T
g.89499C>T
AA changes L106F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 106
frameshift no
known variant Reference ID: rs121918343
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs5376 (pathogenic for Congenital bile acid synthesis defect 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032542)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032542)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032542)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.2520.559
3.0960.908
(flanking)3.8860.905
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 increased89502wt: 0.5290 / mu: 0.5473 (marginal change - not scored)wt: CACTCAGGGTCCTCC
mu: CATTCAGGGTCCTCC		 CTCA|gggt
distance from splice site 55
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      106PEMVRPTLERTLRVLQLDYVDLYI
mutated  not conserved    106PEMVRPTLERTFRVLQLDYVDLY
Ptroglodytes  all identical  ENSPTRG00000019740  106PEMVRPTLERTLRVLQLDYVDLY
Mmulatta  all identical  ENSMMUG00000005422  106PEMVRPTLERTLRVLQLDYVDLY
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038641  105PSMVLPALERTLKALKLDYIDLY
Ggallus  all identical  ENSGALG00000012834  106PELVRPTLEKTLKILQLDYVDLY
Trubripes  all identical  ENSTRUG00000016401  106PELVRPALERTLDELKLDYVDLY
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026269  106PELVRPTLEKTLKTLQLDYVDLY
protein features
start (aa)end (aa)featuredetails 
98109HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 873 / 873
position (AA) of stopcodon in wt / mu AA sequence 291 / 291
position of stopcodon in wt / mu cDNA 960 / 960
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 88 / 88
chromosome 7
strand 1
last intron/exon boundary 943
theoretical NMD boundary in CDS 805
length of CDS 873
coding sequence (CDS) position 316
cDNA position
(for ins/del: last normal base / first normal base)		 403
gDNA position
(for ins/del: last normal base / first normal base)		 89499
chromosomal position
(for ins/del: last normal base / first normal base)		 137776568
original gDNA sequence snippet GCCCAACCCTGGAGAGGACACTCAGGGTCCTCCAGCTAGAT
altered gDNA sequence snippet GCCCAACCCTGGAGAGGACATTCAGGGTCCTCCAGCTAGAT
original cDNA sequence snippet GCCCAACCCTGGAGAGGACACTCAGGGTCCTCCAGCTAGAT
altered cDNA sequence snippet GCCCAACCCTGGAGAGGACATTCAGGGTCCTCCAGCTAGAT
wildtype AA sequence MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTLRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEAMEACKDA GLVKSLGVSN FNRRQLELIL
NKPGLKHKPV SNQVECHPYF TQPKLLKFCQ QHDIVITAYS PLGTSRNPIW VNVSSPPLLK
DALLNSLGKR YNKTAAQIVL RFNIQRGVVV IPKSFNLERI KENFQVARSS *
mutated AA sequence MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTFRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEAMEACKDA GLVKSLGVSN FNRRQLELIL
NKPGLKHKPV SNQVECHPYF TQPKLLKFCQ QHDIVITAYS PLGTSRNPIW VNVSSPPLLK
DALLNSLGKR YNKTAAQIVL RFNIQRGVVV IPKSFNLERI KENFQVARSS *
speed 1.04 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: 0.999994136377947 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032542)
  • known disease mutation: rs5376 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:137776568C>TN/A show variant in all transcripts   IGV
HGNC symbol AKR1D1
Ensembl transcript ID ENST00000411726
Genbank transcript ID NM_001190906
UniProt peptide P51857
alteration type single base exchange
alteration region CDS
DNA changes c.316C>T
cDNA.368C>T
g.89499C>T
AA changes L106F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 106
frameshift no
known variant Reference ID: rs121918343
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs5376 (pathogenic for Congenital bile acid synthesis defect 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032542)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032542)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032542)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.2520.559
3.0960.908
(flanking)3.8860.905
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 increased89502wt: 0.5290 / mu: 0.5473 (marginal change - not scored)wt: CACTCAGGGTCCTCC
mu: CATTCAGGGTCCTCC		 CTCA|gggt
distance from splice site 55
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      106PEMVRPTLERTLRVLQLDYVDLYI
mutated  not conserved    106PEMVRPTLERTFRVLQLDYVDLY
Ptroglodytes  all identical  ENSPTRG00000019740  106PEMVRPTLERTLRVLQLDYVDLY
Mmulatta  all identical  ENSMMUG00000005422  106PEMVRPTLERTLRVLQLDYVDLY
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038641  105PSMVLPALERTLKALKLDYIDLY
Ggallus  all identical  ENSGALG00000012834  106PELVRPTLEKTLKILQLDYVDLY
Trubripes  all identical  ENSTRUG00000016401  106PELVRPALERTLDELKLDYVDLY
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026269  106PELVRPTLEKTLKTLQLDYVDLY
protein features
start (aa)end (aa)featuredetails 
98109HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 858 / 858
position (AA) of stopcodon in wt / mu AA sequence 286 / 286
position of stopcodon in wt / mu cDNA 910 / 910
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 53 / 53
chromosome 7
strand 1
last intron/exon boundary 868
theoretical NMD boundary in CDS 765
length of CDS 858
coding sequence (CDS) position 316
cDNA position
(for ins/del: last normal base / first normal base)		 368
gDNA position
(for ins/del: last normal base / first normal base)		 89499
chromosomal position
(for ins/del: last normal base / first normal base)		 137776568
original gDNA sequence snippet GCCCAACCCTGGAGAGGACACTCAGGGTCCTCCAGCTAGAT
altered gDNA sequence snippet GCCCAACCCTGGAGAGGACATTCAGGGTCCTCCAGCTAGAT
original cDNA sequence snippet GCCCAACCCTGGAGAGGACACTCAGGGTCCTCCAGCTAGAT
altered cDNA sequence snippet GCCCAACCCTGGAGAGGACATTCAGGGTCCTCCAGCTAGAT
wildtype AA sequence MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTLRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEVECHPYFT QPKLLKFCQQ HDIVITAYSP
LGTSRNPIWV NVSSPPLLKD ALLNSLGKRY NKTAAQIVLR FNIQRGVVVI PKSFNLERIK
ENFQIFDFSL TEEEMKDIEA LNKNVRFVEL LMWRDHPEYP FHDEY*
mutated AA sequence MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTFRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEVECHPYFT QPKLLKFCQQ HDIVITAYSP
LGTSRNPIWV NVSSPPLLKD ALLNSLGKRY NKTAAQIVLR FNIQRGVVVI PKSFNLERIK
ENFQIFDFSL TEEEMKDIEA LNKNVRFVEL LMWRDHPEYP FHDEY*
speed 0.98 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: 0.999994136377947 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032542)
  • known disease mutation: rs5376 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:137776568C>TN/A show variant in all transcripts   IGV
HGNC symbol AKR1D1
Ensembl transcript ID ENST00000242375
Genbank transcript ID NM_005989
UniProt peptide P51857
alteration type single base exchange
alteration region CDS
DNA changes c.316C>T
cDNA.358C>T
g.89499C>T
AA changes L106F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 106
frameshift no
known variant Reference ID: rs121918343
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs5376 (pathogenic for Congenital bile acid synthesis defect 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032542)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032542)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032542)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.2520.559
3.0960.908
(flanking)3.8860.905
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 increased89502wt: 0.5290 / mu: 0.5473 (marginal change - not scored)wt: CACTCAGGGTCCTCC
mu: CATTCAGGGTCCTCC		 CTCA|gggt
distance from splice site 55
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      106PEMVRPTLERTLRVLQLDYVDLYI
mutated  not conserved    106PEMVRPTLERTFRVLQLDYVDLY
Ptroglodytes  all identical  ENSPTRG00000019740  106PEMVRPTLERTLRVLQLDYVDLY
Mmulatta  all identical  ENSMMUG00000005422  106PEMVRPTLERTLRVLQLDYVDLY
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038641  105PSMVLPALERTLKALKLDYIDLY
Ggallus  all identical  ENSGALG00000012834  106PELVRPTLEKTLKILQLDYVDLY
Trubripes  all identical  ENSTRUG00000016401  106PELVRPALERTLDELKLDYVDLY
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026269  106PELVRPTLEKTLKTLQLDYVDLY
protein features
start (aa)end (aa)featuredetails 
98109HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 981 / 981
position (AA) of stopcodon in wt / mu AA sequence 327 / 327
position of stopcodon in wt / mu cDNA 1023 / 1023
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 43 / 43
chromosome 7
strand 1
last intron/exon boundary 981
theoretical NMD boundary in CDS 888
length of CDS 981
coding sequence (CDS) position 316
cDNA position
(for ins/del: last normal base / first normal base)		 358
gDNA position
(for ins/del: last normal base / first normal base)		 89499
chromosomal position
(for ins/del: last normal base / first normal base)		 137776568
original gDNA sequence snippet GCCCAACCCTGGAGAGGACACTCAGGGTCCTCCAGCTAGAT
altered gDNA sequence snippet GCCCAACCCTGGAGAGGACATTCAGGGTCCTCCAGCTAGAT
original cDNA sequence snippet GCCCAACCCTGGAGAGGACACTCAGGGTCCTCCAGCTAGAT
altered cDNA sequence snippet GCCCAACCCTGGAGAGGACATTCAGGGTCCTCCAGCTAGAT
wildtype AA sequence MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTLRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEAMEACKDA GLVKSLGVSN FNRRQLELIL
NKPGLKHKPV SNQVECHPYF TQPKLLKFCQ QHDIVITAYS PLGTSRNPIW VNVSSPPLLK
DALLNSLGKR YNKTAAQIVL RFNIQRGVVV IPKSFNLERI KENFQIFDFS LTEEEMKDIE
ALNKNVRFVE LLMWRDHPEY PFHDEY*
mutated AA sequence MDLSAASHRI PLSDGNSIPI IGLGTYSEPK STPKGACATS VKVAIDTGYR HIDGAYIYQN
EHEVGEAIRE KIAEGKVRRE DIFYCGKLWA TNHVPEMVRP TLERTFRVLQ LDYVDLYIIE
VPMAFKPGDE IYPRDENGKW LYHKSNLCAT WEAMEACKDA GLVKSLGVSN FNRRQLELIL
NKPGLKHKPV SNQVECHPYF TQPKLLKFCQ QHDIVITAYS PLGTSRNPIW VNVSSPPLLK
DALLNSLGKR YNKTAAQIVL RFNIQRGVVV IPKSFNLERI KENFQIFDFS LTEEEMKDIE
ALNKNVRFVE LLMWRDHPEY PFHDEY*
speed 0.97 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