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: ENST00000217426
Querying Taster for transcript #2: ENST00000538132
MT speed 0 s - this script 4.663615 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AHCYdisease_causing_automatic0.999999999490003simple_aae0Y143Csingle base exchangers121918608show file
AHCYdisease_causing_automatic0.999999999916318simple_aae0Y115Csingle base exchangers121918608show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999490003 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM045449)
  • known disease mutation: rs12953 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:32880181T>CN/A show variant in all transcripts   IGV
HGNC symbol AHCY
Ensembl transcript ID ENST00000217426
Genbank transcript ID NM_000687
UniProt peptide P23526
alteration type single base exchange
alteration region CDS
DNA changes c.428A>G
cDNA.506A>G
g.19428A>G
AA changes Y143C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 143
frameshift no
known variant Reference ID: rs121918608
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC01111

known disease mutation: rs12953 (pathogenic for Rhabdomyolysis|Hypermethioninemia with s-adenosylhomocysteine hydrolase deficiency|Inborn genetic diseases|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM045449)

known disease mutation at this position, please check HGMD for details (HGMD ID CM045449)
known disease mutation at this position, please check HGMD for details (HGMD ID CM045449)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3541
4.911
(flanking)2.4431
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 increased19420wt: 0.9466 / mu: 0.9585 (marginal change - not scored)wt: ATCCACACCAAGTAC
mu: ATCCACACCAAGTGC		 CCAC|acca
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      143GGDLTNLIHTKYPQLLPGIRGISE
mutated  not conserved    143GGDLTNLIHTKCPQLLPGIRGIS
Ptroglodytes  all identical  ENSPTRG00000013414  143GGDLTNLIHTKYPQLLPGIRGIS
Mmulatta  all identical  ENSMMUG00000005138  143GGDLTNLIHTKYPQLLSGIRGIS
Fcatus  all identical  ENSFCAG00000007301  143DLTNLIHTKYPQLLSGIRGIS
Mmusculus  all identical  ENSMUSG00000027597  143GGDLTNLIHTKYPQLLSGIRGIS
Ggallus  all identical  ENSGALG00000002030  148GGDLTNLVHTKYPQLLKGIRGIS
Trubripes  all identical  ENSTRUG00000002607  149GGDLTNMVHQKYPKLLSGIRGLS
Drerio  all identical  ENSDARG00000005191  143GGDLTNLVHQKYPKLLAGIKGIS
Dmelanogaster  all conserved  FBgn0014455  142GGDLTNLVHEKFPQYLKNIKGLS
Celegans  all identical  K02F2.2  144GGDLTNLVHAKYPQYLAGIRGLS
Xtropicalis  all identical  ENSXETG00000019486  143GGDLTNLVHTKYPQLLKGIKGIS
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1299 / 1299
position (AA) of stopcodon in wt / mu AA sequence 433 / 433
position of stopcodon in wt / mu cDNA 1377 / 1377
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 79 / 79
chromosome 20
strand -1
last intron/exon boundary 1246
theoretical NMD boundary in CDS 1117
length of CDS 1299
coding sequence (CDS) position 428
cDNA position
(for ins/del: last normal base / first normal base)		 506
gDNA position
(for ins/del: last normal base / first normal base)		 19428
chromosomal position
(for ins/del: last normal base / first normal base)		 32880181
original gDNA sequence snippet CAACCTCATCCACACCAAGTACCCGCAGCTTCTGCCAGGTG
altered gDNA sequence snippet CAACCTCATCCACACCAAGTGCCCGCAGCTTCTGCCAGGTG
original cDNA sequence snippet CAACCTCATCCACACCAAGTACCCGCAGCTTCTGCCAGGCA
altered cDNA sequence snippet CAACCTCATCCACACCAAGTGCCCGCAGCTTCTGCCAGGCA
wildtype AA sequence MSDKLPYKVA DIGLAAWGRK ALDIAENEMP GLMRMRERYS ASKPLKGARI AGCLHMTVET
AVLIETLVTL GAEVQWSSCN IFSTQDHAAA AIAKAGIPVY AWKGETDEEY LWCIEQTLYF
KDGPLNMILD DGGDLTNLIH TKYPQLLPGI RGISEETTTG VHNLYKMMAN GILKVPAINV
NDSVTKSKFD NLYGCRESLI DGIKRATDVM IAGKVAVVAG YGDVGKGCAQ ALRGFGARVI
ITEIDPINAL QAAMEGYEVT TMDEACQEGN IFVTTTGCID IILGRHFEQM KDDAIVCNIG
HFDVEIDVKW LNENAVEKVN IKPQVDRYRL KNGRRIILLA EGRLVNLGCA MGHPSFVMSN
SFTNQVMAQI ELWTHPDKYP VGVHFLPKKL DEAVAEAHLG KLNVKLTKLT EKQAQYLGMS
CDGPFKPDHY RY*
mutated AA sequence MSDKLPYKVA DIGLAAWGRK ALDIAENEMP GLMRMRERYS ASKPLKGARI AGCLHMTVET
AVLIETLVTL GAEVQWSSCN IFSTQDHAAA AIAKAGIPVY AWKGETDEEY LWCIEQTLYF
KDGPLNMILD DGGDLTNLIH TKCPQLLPGI RGISEETTTG VHNLYKMMAN GILKVPAINV
NDSVTKSKFD NLYGCRESLI DGIKRATDVM IAGKVAVVAG YGDVGKGCAQ ALRGFGARVI
ITEIDPINAL QAAMEGYEVT TMDEACQEGN IFVTTTGCID IILGRHFEQM KDDAIVCNIG
HFDVEIDVKW LNENAVEKVN IKPQVDRYRL KNGRRIILLA EGRLVNLGCA MGHPSFVMSN
SFTNQVMAQI ELWTHPDKYP VGVHFLPKKL DEAVAEAHLG KLNVKLTKLT EKQAQYLGMS
CDGPFKPDHY RY*
speed 1.19 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: 0.999999999916318 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM045449)
  • known disease mutation: rs12953 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:32880181T>CN/A show variant in all transcripts   IGV
HGNC symbol AHCY
Ensembl transcript ID ENST00000538132
Genbank transcript ID NM_001161766
UniProt peptide P23526
alteration type single base exchange
alteration region CDS
DNA changes c.344A>G
cDNA.731A>G
g.19428A>G
AA changes Y115C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 115
frameshift no
known variant Reference ID: rs121918608
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC01111

known disease mutation: rs12953 (pathogenic for Rhabdomyolysis|Hypermethioninemia with s-adenosylhomocysteine hydrolase deficiency|Inborn genetic diseases|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM045449)

known disease mutation at this position, please check HGMD for details (HGMD ID CM045449)
known disease mutation at this position, please check HGMD for details (HGMD ID CM045449)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3541
4.911
(flanking)2.4431
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 increased19420wt: 0.9466 / mu: 0.9585 (marginal change - not scored)wt: ATCCACACCAAGTAC
mu: ATCCACACCAAGTGC		 CCAC|acca
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      115GGDLTNLIHTKYPQLLPGIRGISE
mutated  not conserved    115GGDLTNLIHTKCPQLLP
Ptroglodytes  all identical  ENSPTRG00000013414  143GGDLTNLIHTKYPQLLP
Mmulatta  all identical  ENSMMUG00000005138  143GGDLTNLIHTKYPQLLS
Fcatus  all identical  ENSFCAG00000007301  143DLTNLIHTKYPQLLSGIRGIS
Mmusculus  all identical  ENSMUSG00000027597  143GGDLTNLIHTKYPQLLS
Ggallus  all identical  ENSGALG00000002030  148GGDLTNLVHTKYPQLL
Trubripes  all identical  ENSTRUG00000002607  149GGDLTNMVHQKYPKLL
Drerio  all identical  ENSDARG00000005191  143GGDLTNLVHQKYPKLL
Dmelanogaster  all conserved  FBgn0014455  142GGDLTNLVHEKFPQYL
Celegans  all identical  K02F2.2  144GGDLTNLVHAKYPQYL
Xtropicalis  all identical  ENSXETG00000019486  143GGDLTNLVHTKYPQLL
protein features
start (aa)end (aa)featuredetails 
107115HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1215 / 1215
position (AA) of stopcodon in wt / mu AA sequence 405 / 405
position of stopcodon in wt / mu cDNA 1602 / 1602
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 388 / 388
chromosome 20
strand -1
last intron/exon boundary 1471
theoretical NMD boundary in CDS 1033
length of CDS 1215
coding sequence (CDS) position 344
cDNA position
(for ins/del: last normal base / first normal base)		 731
gDNA position
(for ins/del: last normal base / first normal base)		 19428
chromosomal position
(for ins/del: last normal base / first normal base)		 32880181
original gDNA sequence snippet CAACCTCATCCACACCAAGTACCCGCAGCTTCTGCCAGGTG
altered gDNA sequence snippet CAACCTCATCCACACCAAGTGCCCGCAGCTTCTGCCAGGTG
original cDNA sequence snippet CAACCTCATCCACACCAAGTACCCGCAGCTTCTGCCAGGCA
altered cDNA sequence snippet CAACCTCATCCACACCAAGTGCCCGCAGCTTCTGCCAGGCA
wildtype AA sequence MPGLMRMRER YSASKPLKGA RIAGCLHMTV ETAVLIETLV TLGAEVQWSS CNIFSTQDHA
AAAIAKAGIP VYAWKGETDE EYLWCIEQTL YFKDGPLNMI LDDGGDLTNL IHTKYPQLLP
GIRGISEETT TGVHNLYKMM ANGILKVPAI NVNDSVTKSK FDNLYGCRES LIDGIKRATD
VMIAGKVAVV AGYGDVGKGC AQALRGFGAR VIITEIDPIN ALQAAMEGYE VTTMDEACQE
GNIFVTTTGC IDIILGRHFE QMKDDAIVCN IGHFDVEIDV KWLNENAVEK VNIKPQVDRY
RLKNGRRIIL LAEGRLVNLG CAMGHPSFVM SNSFTNQVMA QIELWTHPDK YPVGVHFLPK
KLDEAVAEAH LGKLNVKLTK LTEKQAQYLG MSCDGPFKPD HYRY*
mutated AA sequence MPGLMRMRER YSASKPLKGA RIAGCLHMTV ETAVLIETLV TLGAEVQWSS CNIFSTQDHA
AAAIAKAGIP VYAWKGETDE EYLWCIEQTL YFKDGPLNMI LDDGGDLTNL IHTKCPQLLP
GIRGISEETT TGVHNLYKMM ANGILKVPAI NVNDSVTKSK FDNLYGCRES LIDGIKRATD
VMIAGKVAVV AGYGDVGKGC AQALRGFGAR VIITEIDPIN ALQAAMEGYE VTTMDEACQE
GNIFVTTTGC IDIILGRHFE QMKDDAIVCN IGHFDVEIDV KWLNENAVEK VNIKPQVDRY
RLKNGRRIIL LAEGRLVNLG CAMGHPSFVM SNSFTNQVMA QIELWTHPDK YPVGVHFLPK
KLDEAVAEAH LGKLNVKLTK LTEKQAQYLG MSCDGPFKPD HYRY*
speed 1.29 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