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: ENST00000262093
Querying Taster for transcript #2: ENST00000382873
MT speed 0 s - this script 3.79319 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FECHdisease_causing_automatic0.999999892612615simple_aae0F423Ssingle base exchangers118204039show file
FECHdisease_causing_automatic0.999999982379628simple_aae0F417Ssingle base exchangers118204039show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999892612615 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920271)
  • known disease mutation: rs551 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:55217966A>GN/A show variant in all transcripts   IGV
HGNC symbol FECH
Ensembl transcript ID ENST00000382873
Genbank transcript ID NM_001012515
UniProt peptide P22830
alteration type single base exchange
alteration region CDS
DNA changes c.1268T>C
cDNA.1302T>C
g.36039T>C
AA changes F423S Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 423
frameshift no
known variant Reference ID: rs118204039
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs551 (pathogenic for Protoporphyria, erythropoietic, 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920271)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920271)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920271)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7481
4.7591
(flanking)4.7591
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 113
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      423CVNPVCRETKSFFTSQQL*
mutated  not conserved    423KSSFTSQQL
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000022568  423KSFFTSQQL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000024588  416KSFFTSQQL
Ggallus  all identical  ENSGALG00000003066  407CVNPVCRETKAFFT
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000003462  403CVNPTCAQTKAFFSSQKL
Dmelanogaster  all conserved  FBgn0024891  377CSNPKCRESKSWY
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020888  411CVNPVCGEAKSFFTKQQ
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1290 / 1290
position (AA) of stopcodon in wt / mu AA sequence 430 / 430
position of stopcodon in wt / mu cDNA 1324 / 1324
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 35 / 35
chromosome 18
strand -1
last intron/exon boundary 1190
theoretical NMD boundary in CDS 1105
length of CDS 1290
coding sequence (CDS) position 1268
cDNA position
(for ins/del: last normal base / first normal base)		 1302
gDNA position
(for ins/del: last normal base / first normal base)		 36039
chromosomal position
(for ins/del: last normal base / first normal base)		 55217966
original gDNA sequence snippet CTGCAGGGAGACTAAATCCTTCTTCACCAGCCAGCAGCTGT
altered gDNA sequence snippet CTGCAGGGAGACTAAATCCTCCTTCACCAGCCAGCAGCTGT
original cDNA sequence snippet CTGCAGGGAGACTAAATCCTTCTTCACCAGCCAGCAGCTGT
altered cDNA sequence snippet CTGCAGGGAGACTAAATCCTCCTTCACCAGCCAGCAGCTGT
wildtype AA sequence MRSLGANMAA ALRAAGVLLR DPLASSSWRV CQPWRWKSGA AAAAVTTETA QHAQGAKPQV
QPQKRYESNI RKPKTGILML NMGGPETLGD VHDFLLRLFL DRDLMTLPIQ NKLAPFIAKR
RTPKIQEQYR RIGGGSPIKI WTSKQGEGMV KLLDELSPNT APHKYYIGFR YVHPLTEEAI
EEMERDGLER AIAFTQYPQY SCSTTGSSLN AIYRYYNQVG RKPTMKWSTI DRWPTHHLLI
QCFADHILKE LDHFPLEKRS EVVILFSAHS LPMSVVNRGD PYPQEVSATV QKVMERLEYC
NPYRLVWQSK VGPMPWLGPQ TDESIKGLCE RGRKNILLVP IAFTSDHIET LYELDIEYSQ
VLAKECGVEN IRRAESLNGN PLFSKALADL VHSHIQSNEL CSKQLTLSCP LCVNPVCRET
KSFFTSQQL*
mutated AA sequence MRSLGANMAA ALRAAGVLLR DPLASSSWRV CQPWRWKSGA AAAAVTTETA QHAQGAKPQV
QPQKRYESNI RKPKTGILML NMGGPETLGD VHDFLLRLFL DRDLMTLPIQ NKLAPFIAKR
RTPKIQEQYR RIGGGSPIKI WTSKQGEGMV KLLDELSPNT APHKYYIGFR YVHPLTEEAI
EEMERDGLER AIAFTQYPQY SCSTTGSSLN AIYRYYNQVG RKPTMKWSTI DRWPTHHLLI
QCFADHILKE LDHFPLEKRS EVVILFSAHS LPMSVVNRGD PYPQEVSATV QKVMERLEYC
NPYRLVWQSK VGPMPWLGPQ TDESIKGLCE RGRKNILLVP IAFTSDHIET LYELDIEYSQ
VLAKECGVEN IRRAESLNGN PLFSKALADL VHSHIQSNEL CSKQLTLSCP LCVNPVCRET
KSSFTSQQL*
speed 0.69 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: 0.999999982379628 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920271)
  • known disease mutation: rs551 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:55217966A>GN/A show variant in all transcripts   IGV
HGNC symbol FECH
Ensembl transcript ID ENST00000262093
Genbank transcript ID NM_000140
UniProt peptide P22830
alteration type single base exchange
alteration region CDS
DNA changes c.1250T>C
cDNA.1402T>C
g.36039T>C
AA changes F417S Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 417
frameshift no
known variant Reference ID: rs118204039
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs551 (pathogenic for Protoporphyria, erythropoietic, 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920271)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920271)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920271)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7481
4.7591
(flanking)4.7591
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 113
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      417CVNPVCRETKSFFTSQQL*
mutated  not conserved    417CVNPVCRETKSSFTS
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000022568  423KSFFTSQQL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000024588  416CVNPVCRKTKSFFTS
Ggallus  all identical  ENSGALG00000003066  407CVNPVCRETKAFFTNQQL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000003462  403CVNPTCAQTKAFFSSQKL
Dmelanogaster  all conserved  FBgn0024891  377CSNPKCRESKSWY
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020888  411CVNPVCGEAKSFFTKQQ
protein features
start (aa)end (aa)featuredetails 
410419HELIXlost
417417MUTAGENF->L: Decreased activity.lost
417417MUTAGENF->Y,W: Greatly reduced activity.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1272 / 1272
position (AA) of stopcodon in wt / mu AA sequence 424 / 424
position of stopcodon in wt / mu cDNA 1424 / 1424
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 153 / 153
chromosome 18
strand -1
last intron/exon boundary 1290
theoretical NMD boundary in CDS 1087
length of CDS 1272
coding sequence (CDS) position 1250
cDNA position
(for ins/del: last normal base / first normal base)		 1402
gDNA position
(for ins/del: last normal base / first normal base)		 36039
chromosomal position
(for ins/del: last normal base / first normal base)		 55217966
original gDNA sequence snippet CTGCAGGGAGACTAAATCCTTCTTCACCAGCCAGCAGCTGT
altered gDNA sequence snippet CTGCAGGGAGACTAAATCCTCCTTCACCAGCCAGCAGCTGT
original cDNA sequence snippet CTGCAGGGAGACTAAATCCTTCTTCACCAGCCAGCAGCTGT
altered cDNA sequence snippet CTGCAGGGAGACTAAATCCTCCTTCACCAGCCAGCAGCTGT
wildtype AA sequence MRSLGANMAA ALRAAGVLLR DPLASSSWRV CQPWRWKSGA AAAAVTTETA QHAQGAKPQV
QPQKRKPKTG ILMLNMGGPE TLGDVHDFLL RLFLDRDLMT LPIQNKLAPF IAKRRTPKIQ
EQYRRIGGGS PIKIWTSKQG EGMVKLLDEL SPNTAPHKYY IGFRYVHPLT EEAIEEMERD
GLERAIAFTQ YPQYSCSTTG SSLNAIYRYY NQVGRKPTMK WSTIDRWPTH HLLIQCFADH
ILKELDHFPL EKRSEVVILF SAHSLPMSVV NRGDPYPQEV SATVQKVMER LEYCNPYRLV
WQSKVGPMPW LGPQTDESIK GLCERGRKNI LLVPIAFTSD HIETLYELDI EYSQVLAKEC
GVENIRRAES LNGNPLFSKA LADLVHSHIQ SNELCSKQLT LSCPLCVNPV CRETKSFFTS
QQL*
mutated AA sequence MRSLGANMAA ALRAAGVLLR DPLASSSWRV CQPWRWKSGA AAAAVTTETA QHAQGAKPQV
QPQKRKPKTG ILMLNMGGPE TLGDVHDFLL RLFLDRDLMT LPIQNKLAPF IAKRRTPKIQ
EQYRRIGGGS PIKIWTSKQG EGMVKLLDEL SPNTAPHKYY IGFRYVHPLT EEAIEEMERD
GLERAIAFTQ YPQYSCSTTG SSLNAIYRYY NQVGRKPTMK WSTIDRWPTH HLLIQCFADH
ILKELDHFPL EKRSEVVILF SAHSLPMSVV NRGDPYPQEV SATVQKVMER LEYCNPYRLV
WQSKVGPMPW LGPQTDESIK GLCERGRKNI LLVPIAFTSD HIETLYELDI EYSQVLAKEC
GVENIRRAES LNGNPLFSKA LADLVHSHIQ SNELCSKQLT LSCPLCVNPV CRETKSSFTS
QQL*
speed 1.10 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