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 2.72 s - this script 7.291323 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ALADdisease_causing0.999613880574255simple_aaeF12Lsingle base exchangers121912984show file
ALADdisease_causing0.999613880574255simple_aaeF12Lsingle base exchangers121912984show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999613880574255      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs16867 (probable pathogenic)
  • known disease mutation at this position (HGMD CM992131)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:116155804G>CN/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.36C>G
cDNA.233C>G
g.7810C>G
AA changes F12L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS
12
frameshift no
known variant Reference ID: rs121912984
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC044

known as potential disease variant: rs16867 (probable pathogenic for Porphyria, acute hepatic, digenic|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992131)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992131)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992131)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1751
1.7951
(flanking)4.2981
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 78
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      12MQPQSVLHSGYFHPLLRAWQTATT
mutated  not conserved    12MQPQSVLHSGYLHPLLRAWQTAT
Ptroglodytes  no homologue    
Mmulatta  no alignment  ENSMMUG00000031965  n/a
Fcatus  no alignment  ENSFCAG00000009244  n/a
Mmusculus  all identical  ENSMUSG00000028393  12MHHQSVLHSGYFHPLLRSWQTAA
Ggallus  all identical  ENSGALG00000008869  19MQADSLLHSGYFHPVLRSWQCTA
Trubripes  all identical  ENSTRUG00000010590  21PQSILHSGYFHPTLRYWQTCA
Drerio  all identical  ENSDARG00000052815  14ESILHSGYFHPTLRYWQTCA
Dmelanogaster  not conserved  FBgn0036271  10LHSGMHHATLRQLQESG
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000023474  n/a
protein features no protein features affected
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 36
cDNA position
(for ins/del: last normal base / first normal base)
233
gDNA position
(for ins/del: last normal base / first normal base)
7810
chromosomal position
(for ins/del: last normal base / first normal base)
116155804
original gDNA sequence snippet GTTCTGCACAGCGGCTACTTCCACCCACTACTTCGGGCCTG
altered gDNA sequence snippet GTTCTGCACAGCGGCTACTTGCACCCACTACTTCGGGCCTG
original cDNA sequence snippet GTTCTGCACAGCGGCTACTTCCACCCACTACTTCGGGCCTG
altered cDNA sequence snippet GTTCTGCACAGCGGCTACTTGCACCCACTACTTCGGGCCTG
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 YLHPLLRAWQ 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 *
speed 1.30 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: 0.999613880574255      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs16867 (probable pathogenic)
  • known disease mutation at this position (HGMD CM992131)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:116155804G>CN/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.36C>G
cDNA.298C>G
g.7810C>G
AA changes F12L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS
12
frameshift no
known variant Reference ID: rs121912984
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC044

known as potential disease variant: rs16867 (probable pathogenic for Porphyria, acute hepatic, digenic|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992131)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992131)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992131)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1751
1.7951
(flanking)4.2981
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 78
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      12MQPQSVLHSGYFHPLLRAWQTATT
mutated  not conserved    12MQPQSVLHSGYLHPLLRAWQTAT
Ptroglodytes  no homologue    
Mmulatta  no alignment  ENSMMUG00000031965  n/a
Fcatus  no alignment  ENSFCAG00000009244  n/a
Mmusculus  all identical  ENSMUSG00000028393  12MHHQSVLHSGYFHPLLRSWQTAA
Ggallus  all identical  ENSGALG00000008869  19MQADSLLHSGYFHPVLRSWQCTA
Trubripes  all identical  ENSTRUG00000010590  21PQSILHSGYFHPTLRYWQTCA
Drerio  all identical  ENSDARG00000052815  14ESILHSGYFHPTLRYWQTCA
Dmelanogaster  not conserved  FBgn0036271  10LHSGMHHATLRQLQESG
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000023474  n/a
protein features no protein features affected
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 36
cDNA position
(for ins/del: last normal base / first normal base)
298
gDNA position
(for ins/del: last normal base / first normal base)
7810
chromosomal position
(for ins/del: last normal base / first normal base)
116155804
original gDNA sequence snippet GTTCTGCACAGCGGCTACTTCCACCCACTACTTCGGGCCTG
altered gDNA sequence snippet GTTCTGCACAGCGGCTACTTGCACCCACTACTTCGGGCCTG
original cDNA sequence snippet GTTCTGCACAGCGGCTACTTCCACCCACTACTTCGGGCCTG
altered cDNA sequence snippet GTTCTGCACAGCGGCTACTTGCACCCACTACTTCGGGCCTG
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 YLHPLLRAWQ 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*
speed 1.42 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