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: ENST00000409155
Querying Taster for transcript #2: ENST00000277315
MT speed 0 s - this script 4.187005 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ALADdisease_causing_automatic0.999999993766523simple_aaeaffected0G133Rsingle base exchangers121912980show file
ALADdisease_causing_automatic0.999999998623678simple_aaeaffected0G116Rsingle base exchangers121912980show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999993766523 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910019)
  • known disease mutation: rs16862 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:116153078C>TN/A show variant in all transcripts   IGV
HGNC symbol ALAD
Ensembl transcript ID ENST00000409155
Genbank transcript ID NM_000031
UniProt peptide P13716
alteration type single base exchange
alteration region CDS
DNA changes c.397G>A
cDNA.594G>A
g.10536G>A
AA changes G133R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 133
frameshift no
known variant Reference ID: rs121912980
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs16862 (pathogenic for Porphobilinogen synthase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910019)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.4331
2.760.996
(flanking)-0.8950.627
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost10536sequence motif lost- wt: TGCG|gtga
 mu: TGCA.gtga
Acc marginally increased10526wt: 0.8708 / mu: 0.8879 (marginal change - not scored)wt: CTGTGTCCCTACACCTCCCATGGTCACTGCGGTGAGTTCCC
mu: CTGTGTCCCTACACCTCCCATGGTCACTGCAGTGAGTTCCC		 ccat|GGTC
Acc marginally increased10537wt: 0.2161 / mu: 0.2371 (marginal change - not scored)wt: CACCTCCCATGGTCACTGCGGTGAGTTCCCTCCCTCCCACC
mu: CACCTCCCATGGTCACTGCAGTGAGTTCCCTCCCTCCCACC		 gcgg|TGAG
Donor increased10533wt: 0.45 / mu: 0.49wt: GTCACTGCGGTGAGT
mu: GTCACTGCAGTGAGT		 CACT|gcgg
Donor gained105310.79mu: TGGTCACTGCAGTGA GTCA|ctgc
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      133CLCPYTSHGHCGLLSENGAFRAEE
mutated  not conserved    133CLCPYTSHGHCRLLSENGAFRAE
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000031965  162CLCPYTSHGHCGLLSENGAFRAE
Fcatus  all identical  ENSFCAG00000009244  149CLCPYTSHGHCGLLGKNGTFQAE
Mmusculus  all identical  ENSMUSG00000028393  133CLCPYTSHGHCGLLSENGAFLAE
Ggallus  all identical  ENSGALG00000008869  140CLCPYTSHGHCGILREDGTIQNE
Trubripes  all identical  ENSTRUG00000010590  142LCPYTSHGHCGILNDDGTLNND
Drerio  all identical  ENSDARG00000052815  135CPYTSHGHCGILREDGSLDNA
Dmelanogaster  all identical  FBgn0036271  131SSHGHCGLLGETGLENGP
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023474  79CLCPYTSHGHCGILREDGSLQNE
protein features
start (aa)end (aa)featuredetails 
131131METALZinc 2.might get lost (downstream of altered splice site)
131131MUTAGENH->A: No effect on catalytic activity; when associated with A-223.might get lost (downstream of altered splice site)
132132MUTAGENC->A: Reduces enzyme activity about 1000000-fold; when associated with A-122 and A-124.might get lost (downstream of altered splice site)
132132METALZinc 1; catalytic.might get lost (downstream of altered splice site)
141160HELIXmight get lost (downstream of altered splice site)
163167STRANDmight get lost (downstream of altered splice site)
174184HELIXmight get lost (downstream of altered splice site)
188190TURNmight get lost (downstream of altered splice site)
192194STRANDmight get lost (downstream of altered splice site)
198200STRANDmight get lost (downstream of altered splice site)
199199ACT_SITESchiff-base intermediate with substrate.might get lost (downstream of altered splice site)
203205HELIXmight get lost (downstream of altered splice site)
206210HELIXmight get lost (downstream of altered splice site)
209209BINDINGSubstrate 1.might get lost (downstream of altered splice site)
221221BINDINGSubstrate 1.might get lost (downstream of altered splice site)
221223HELIXmight get lost (downstream of altered splice site)
223223METALZinc 2.might get lost (downstream of altered splice site)
223223MUTAGENC->A: No effect on catalytic activity; when associated with A-131.might get lost (downstream of altered splice site)
231243HELIXmight get lost (downstream of altered splice site)
247253STRANDmight get lost (downstream of altered splice site)
252252ACT_SITESchiff-base intermediate with substrate.might get lost (downstream of altered splice site)
255257HELIXmight get lost (downstream of altered splice site)
258267HELIXmight get lost (downstream of altered splice site)
273277STRANDmight get lost (downstream of altered splice site)
279279BINDINGSubstrate 2.might get lost (downstream of altered splice site)
279290HELIXmight get lost (downstream of altered splice site)
296310HELIXmight get lost (downstream of altered splice site)
313317STRANDmight get lost (downstream of altered splice site)
318318BINDINGSubstrate 2.might get lost (downstream of altered splice site)
320326HELIXmight get lost (downstream of altered splice site)
327329TURNmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 993 / 993
position (AA) of stopcodon in wt / mu AA sequence 331 / 331
position of stopcodon in wt / mu cDNA 1190 / 1190
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 198 / 198
chromosome 9
strand -1
last intron/exon boundary 1129
theoretical NMD boundary in CDS 881
length of CDS 993
coding sequence (CDS) position 397
cDNA position
(for ins/del: last normal base / first normal base)		 594
gDNA position
(for ins/del: last normal base / first normal base)		 10536
chromosomal position
(for ins/del: last normal base / first normal base)		 116153078
original gDNA sequence snippet ACACCTCCCATGGTCACTGCGGTGAGTTCCCTCCCTCCCAC
altered gDNA sequence snippet ACACCTCCCATGGTCACTGCAGTGAGTTCCCTCCCTCCCAC
original cDNA sequence snippet ACACCTCCCATGGTCACTGCGGGCTCCTGAGTGAAAACGGA
altered cDNA sequence snippet ACACCTCCCATGGTCACTGCAGGCTCCTGAGTGAAAACGGA
wildtype AA sequence MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTDV PDDIQPITSL PGVARYGVKR
LEEMLRPLVE EGLRCVLIFG VPSRVPKDER GSAADSEESP AIEAIHLLRK TFPNLLVACD
VCLCPYTSHG HCGLLSENGA FRAEESRQRL AEVALAYAKA GCQVVAPSDM MDGRVEAIKE
ALMAHGLGNR VSVMSYSAKF ASCFYGPFRD AAKSSPAFGD RRCYQLPPGA RGLALRAVDR
DVREGADMLM VKPGMPYLDI VREVKDKHPD LPLAVYHVSG EFAMLWHGAQ AGAFDLKAAV
LEAMTAFRRA GADIIITYYT PQLLQWLKEE *
mutated AA sequence MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTDV PDDIQPITSL PGVARYGVKR
LEEMLRPLVE EGLRCVLIFG VPSRVPKDER GSAADSEESP AIEAIHLLRK TFPNLLVACD
VCLCPYTSHG HCRLLSENGA FRAEESRQRL AEVALAYAKA GCQVVAPSDM MDGRVEAIKE
ALMAHGLGNR VSVMSYSAKF ASCFYGPFRD AAKSSPAFGD RRCYQLPPGA RGLALRAVDR
DVREGADMLM VKPGMPYLDI VREVKDKHPD LPLAVYHVSG EFAMLWHGAQ AGAFDLKAAV
LEAMTAFRRA GADIIITYYT PQLLQWLKEE *
speed 0.91 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: 0.999999998623678 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910019)
  • known disease mutation: rs16862 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:116153078C>TN/A show variant in all transcripts   IGV
HGNC symbol ALAD
Ensembl transcript ID ENST00000277315
Genbank transcript ID N/A
UniProt peptide P13716
alteration type single base exchange
alteration region CDS
DNA changes c.346G>A
cDNA.608G>A
g.10536G>A
AA changes G116R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 116
frameshift no
known variant Reference ID: rs121912980
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs16862 (pathogenic for Porphobilinogen synthase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910019)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.4331
2.760.996
(flanking)-0.8950.627
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost10536sequence motif lost- wt: TGCG|gtga
 mu: TGCA.gtga
Acc marginally increased10526wt: 0.8708 / mu: 0.8879 (marginal change - not scored)wt: CTGTGTCCCTACACCTCCCATGGTCACTGCGGTGAGTTCCC
mu: CTGTGTCCCTACACCTCCCATGGTCACTGCAGTGAGTTCCC		 ccat|GGTC
Acc marginally increased10537wt: 0.2161 / mu: 0.2371 (marginal change - not scored)wt: CACCTCCCATGGTCACTGCGGTGAGTTCCCTCCCTCCCACC
mu: CACCTCCCATGGTCACTGCAGTGAGTTCCCTCCCTCCCACC		 gcgg|TGAG
Donor increased10533wt: 0.45 / mu: 0.49wt: GTCACTGCGGTGAGT
mu: GTCACTGCAGTGAGT		 CACT|gcgg
Donor gained105310.79mu: TGGTCACTGCAGTGA GTCA|ctgc
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      116CLCPYTSHGHCGLLSENGAFRAEE
mutated  not conserved    116CLCPYTSHGHCRLLSE
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000031965  162CLCPYTSHGHCGLLSENGAFRAE
Fcatus  all identical  ENSFCAG00000009244  149CLCPYTSHGHCGLLGKNGTFQAE
Mmusculus  all identical  ENSMUSG00000028393  133CLCPYTSHGHCGLLSENGAFLAE
Ggallus  all identical  ENSGALG00000008869  140CLCPYTSHGHCGILREDGTIQNE
Trubripes  all identical  ENSTRUG00000010590  142LCPYTSHGHCGILNDDGTLNND
Drerio  all identical  ENSDARG00000052815  135CPYTSHGHCGILREDGSLDNA
Dmelanogaster  all identical  FBgn0036271  131SSHGHCGLLGETGLENGP
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023474  79CLCPYTSHGHCGILREDGSLQNE
protein features
start (aa)end (aa)featuredetails 
115121STRANDlost
122122MUTAGENC->A: Reduces enzyme activity about 1000000-fold; when associated with A-124 and A-132.might get lost (downstream of altered splice site)
122122METALZinc 1; catalytic.might get lost (downstream of altered splice site)
123126STRANDmight get lost (downstream of altered splice site)
124124MUTAGENC->A: Reduces enzyme activity about 1000000-fold; when associated with A-122 and A-132.might get lost (downstream of altered splice site)
124124METALZinc 1; catalytic.might get lost (downstream of altered splice site)
131131METALZinc 2.might get lost (downstream of altered splice site)
131131MUTAGENH->A: No effect on catalytic activity; when associated with A-223.might get lost (downstream of altered splice site)
132132METALZinc 1; catalytic.might get lost (downstream of altered splice site)
132132MUTAGENC->A: Reduces enzyme activity about 1000000-fold; when associated with A-122 and A-124.might get lost (downstream of altered splice site)
141160HELIXmight get lost (downstream of altered splice site)
163167STRANDmight get lost (downstream of altered splice site)
174184HELIXmight get lost (downstream of altered splice site)
188190TURNmight get lost (downstream of altered splice site)
192194STRANDmight get lost (downstream of altered splice site)
198200STRANDmight get lost (downstream of altered splice site)
199199ACT_SITESchiff-base intermediate with substrate.might get lost (downstream of altered splice site)
203205HELIXmight get lost (downstream of altered splice site)
206210HELIXmight get lost (downstream of altered splice site)
209209BINDINGSubstrate 1.might get lost (downstream of altered splice site)
221221BINDINGSubstrate 1.might get lost (downstream of altered splice site)
221223HELIXmight get lost (downstream of altered splice site)
223223METALZinc 2.might get lost (downstream of altered splice site)
223223MUTAGENC->A: No effect on catalytic activity; when associated with A-131.might get lost (downstream of altered splice site)
231243HELIXmight get lost (downstream of altered splice site)
247253STRANDmight get lost (downstream of altered splice site)
252252ACT_SITESchiff-base intermediate with substrate.might get lost (downstream of altered splice site)
255257HELIXmight get lost (downstream of altered splice site)
258267HELIXmight get lost (downstream of altered splice site)
273277STRANDmight get lost (downstream of altered splice site)
279279BINDINGSubstrate 2.might get lost (downstream of altered splice site)
279290HELIXmight get lost (downstream of altered splice site)
296310HELIXmight get lost (downstream of altered splice site)
313317STRANDmight get lost (downstream of altered splice site)
318318BINDINGSubstrate 2.might get lost (downstream of altered splice site)
320326HELIXmight get lost (downstream of altered splice site)
327329TURNmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 942 / 942
position (AA) of stopcodon in wt / mu AA sequence 314 / 314
position of stopcodon in wt / mu cDNA 1204 / 1204
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 263 / 263
chromosome 9
strand -1
last intron/exon boundary 1143
theoretical NMD boundary in CDS 830
length of CDS 942
coding sequence (CDS) position 346
cDNA position
(for ins/del: last normal base / first normal base)		 608
gDNA position
(for ins/del: last normal base / first normal base)		 10536
chromosomal position
(for ins/del: last normal base / first normal base)		 116153078
original gDNA sequence snippet ACACCTCCCATGGTCACTGCGGTGAGTTCCCTCCCTCCCAC
altered gDNA sequence snippet ACACCTCCCATGGTCACTGCAGTGAGTTCCCTCCCTCCCAC
original cDNA sequence snippet ACACCTCCCATGGTCACTGCGGGCTCCTGAGTGAAAACGGA
altered cDNA sequence snippet ACACCTCCCATGGTCACTGCAGGCTCCTGAGTGAAAACGGA
wildtype AA sequence MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTYG VKRLEEMLRP LVEEGLRCVL
IFGVPSRVPK DERGSAADSE ESPAIEAIHL LRKTFPNLLV ACDVCLCPYT SHGHCGLLSE
NGAFRAEESR QRLAEVALAY AKAGCQVVAP SDMMDGRVEA IKEALMAHGL GNRVSVMSYS
AKFASCFYGP FRDAAKSSPA FGDRRCYQLP PGARGLALRA VDRDVREGAD MLMVKPGMPY
LDIVREVKDK HPDLPLAVYH VSGEFAMLWH GAQAGAFDLK AAVLEAMTAF RRAGADIIIT
YYTPQLLQWL KEE*
mutated AA sequence MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTYG VKRLEEMLRP LVEEGLRCVL
IFGVPSRVPK DERGSAADSE ESPAIEAIHL LRKTFPNLLV ACDVCLCPYT SHGHCRLLSE
NGAFRAEESR QRLAEVALAY AKAGCQVVAP SDMMDGRVEA IKEALMAHGL GNRVSVMSYS
AKFASCFYGP FRDAAKSSPA FGDRRCYQLP PGARGLALRA VDRDVREGAD MLMVKPGMPY
LDIVREVKDK HPDLPLAVYH VSGEFAMLWH GAQAGAFDLK AAVLEAMTAF RRAGADIIIT
YYTPQLLQWL KEE*
speed 1.28 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