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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: ENST00000376131
Querying Taster for transcript #2: ENST00000376143
MT speed 3.08 s - this script 8.597406 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF14disease_causing_automatic0.999999984023968simple_aaeaffected0F150Ssingle base exchangers104894393show file
FGF14disease_causing_automatic0.999999984023968simple_aaeaffected0F145Ssingle base exchangers104894393show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999984023968 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030039)
  • known disease mutation: rs8115 (pathogenic)
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:102379135A>GN/A show variant in all transcripts   IGV
HGNC symbol FGF14
Ensembl transcript ID ENST00000376131
Genbank transcript ID NM_175929
UniProt peptide Q92915
alteration type single base exchange
alteration region CDS
DNA changes c.449T>C
cDNA.545T>C
g.674990T>C
AA changes F150S Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS
150
frameshift no
known variant Reference ID: rs104894393
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8115 (pathogenic for Spinocerebellar ataxia type 27) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030039)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030039)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030039)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0871
4.8781
(flanking)4.8781
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased674981wt: 0.8167 / mu: 0.8272 (marginal change - not scored)wt: ACAGGAACTTTTTACCCCTGAATGCAAGTTTAAAGAATCTG
mu: ACAGGAACTTTTTACCCCTGAATGCAAGTCTAAAGAATCTG
 ctga|ATGC
Donor marginally increased674987wt: 0.2557 / mu: 0.3389 (marginal change - not scored)wt: ATGCAAGTTTAAAGA
mu: ATGCAAGTCTAAAGA
 GCAA|gttt
Donor marginally increased674982wt: 0.9934 / mu: 0.9954 (marginal change - not scored)wt: CCTGAATGCAAGTTT
mu: CCTGAATGCAAGTCT
 TGAA|tgca
Donor increased674989wt: 0.69 / mu: 0.88wt: GCAAGTTTAAAGAAT
mu: GCAAGTCTAAAGAAT
 AAGT|ttaa
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      150YPSELFTPECKFKESVFENYYVIY
mutated  not conserved    150YPSELFTPECKSKESVFENYYVI
Ptroglodytes  all identical  ENSPTRG00000006008  150YPSELFTPECKFKESVFENYYVI
Mmulatta  all identical  ENSMMUG00000002875  150YPSELFTPECKFKESVFENYYVI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000025551  150YPSELFTPECKFKESVFENYYVI
Ggallus  all identical  ENSGALG00000016866  150YTSELFTPECKFKESVFENYYVI
Trubripes  all identical  ENSTRUG00000012467  146YTSELFTAECKFKESVFENYYVI
Drerio  all identical  ENSDARG00000040982  145YTSELFTPECKFKESVFENYYVI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020664  145YTSELFTLECKFKESVFENYYVI
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 759 / 759
position (AA) of stopcodon in wt / mu AA sequence 253 / 253
position of stopcodon in wt / mu cDNA 855 / 855
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 97 / 97
chromosome 13
strand -1
last intron/exon boundary 719
theoretical NMD boundary in CDS 572
length of CDS 759
coding sequence (CDS) position 449
cDNA position
(for ins/del: last normal base / first normal base)
545
gDNA position
(for ins/del: last normal base / first normal base)
674990
chromosomal position
(for ins/del: last normal base / first normal base)
102379135
original gDNA sequence snippet TTTTACCCCTGAATGCAAGTTTAAAGAATCTGTTTTTGAAA
altered gDNA sequence snippet TTTTACCCCTGAATGCAAGTCTAAAGAATCTGTTTTTGAAA
original cDNA sequence snippet TTTTACCCCTGAATGCAAGTTTAAAGAATCTGTTTTTGAAA
altered cDNA sequence snippet TTTTACCCCTGAATGCAAGTCTAAAGAATCTGTTTTTGAAA
wildtype AA sequence MVKPVPLFRR TDFKLLLCNH KDLFFLRVSK LLDCFSPKSM WFLWNIFSKG THMLQCLCGK
SLKKNKNPTD PQLKGIVTRL YCRQGYYLQM HPDGALDGTK DDSTNSTLFN LIPVGLRVVA
IQGVKTGLYI AMNGEGYLYP SELFTPECKF KESVFENYYV IYSSMLYRQQ ESGRAWFLGL
NKEGQAMKGN RVKKTKPAAH FLPKPLEVAM YREPSLHDVG ETVPKPGVTP SKSTSASAIM
NGGKPVNKSK TT*
mutated AA sequence MVKPVPLFRR TDFKLLLCNH KDLFFLRVSK LLDCFSPKSM WFLWNIFSKG THMLQCLCGK
SLKKNKNPTD PQLKGIVTRL YCRQGYYLQM HPDGALDGTK DDSTNSTLFN LIPVGLRVVA
IQGVKTGLYI AMNGEGYLYP SELFTPECKS KESVFENYYV IYSSMLYRQQ ESGRAWFLGL
NKEGQAMKGN RVKKTKPAAH FLPKPLEVAM YREPSLHDVG ETVPKPGVTP SKSTSASAIM
NGGKPVNKSK TT*
speed 1.41 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: 0.999999984023968 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030039)
  • known disease mutation: rs8115 (pathogenic)
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:102379135A>GN/A show variant in all transcripts   IGV
HGNC symbol FGF14
Ensembl transcript ID ENST00000376143
Genbank transcript ID NM_004115
UniProt peptide Q92915
alteration type single base exchange
alteration region CDS
DNA changes c.434T>C
cDNA.434T>C
g.674990T>C
AA changes F145S Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS
145
frameshift no
known variant Reference ID: rs104894393
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8115 (pathogenic for Spinocerebellar ataxia type 27) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030039)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030039)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030039)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0871
4.8781
(flanking)4.8781
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased674981wt: 0.8167 / mu: 0.8272 (marginal change - not scored)wt: ACAGGAACTTTTTACCCCTGAATGCAAGTTTAAAGAATCTG
mu: ACAGGAACTTTTTACCCCTGAATGCAAGTCTAAAGAATCTG
 ctga|ATGC
Donor marginally increased674987wt: 0.2557 / mu: 0.3389 (marginal change - not scored)wt: ATGCAAGTTTAAAGA
mu: ATGCAAGTCTAAAGA
 GCAA|gttt
Donor marginally increased674982wt: 0.9934 / mu: 0.9954 (marginal change - not scored)wt: CCTGAATGCAAGTTT
mu: CCTGAATGCAAGTCT
 TGAA|tgca
Donor increased674989wt: 0.69 / mu: 0.88wt: GCAAGTTTAAAGAAT
mu: GCAAGTCTAAAGAAT
 AAGT|ttaa
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      145YPSELFTPECKFKESVFENYYVIY
mutated  not conserved    145YPSELFTPECKSKESVFENYYVI
Ptroglodytes  all identical  ENSPTRG00000006008  150YPSELFTPECKFKESVFENYYVI
Mmulatta  all identical  ENSMMUG00000002875  150YPSELFTPECKFKESVFENYYVI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000025551  150YPSELFTPECKFKESVFENYYVI
Ggallus  all identical  ENSGALG00000016866  150YTSELFTPECKFKESVFENYYVI
Trubripes  all identical  ENSTRUG00000012467  146YTSELFTAECKFKESVFENYYVI
Drerio  all identical  ENSDARG00000040982  145YTSELFTPECKFKESVFENYYVI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020664  145YTSELFTLECKFKESVFENYYVI
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 744 / 744
position (AA) of stopcodon in wt / mu AA sequence 248 / 248
position of stopcodon in wt / mu cDNA 744 / 744
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 1 / 1
chromosome 13
strand -1
last intron/exon boundary 608
theoretical NMD boundary in CDS 557
length of CDS 744
coding sequence (CDS) position 434
cDNA position
(for ins/del: last normal base / first normal base)
434
gDNA position
(for ins/del: last normal base / first normal base)
674990
chromosomal position
(for ins/del: last normal base / first normal base)
102379135
original gDNA sequence snippet TTTTACCCCTGAATGCAAGTTTAAAGAATCTGTTTTTGAAA
altered gDNA sequence snippet TTTTACCCCTGAATGCAAGTCTAAAGAATCTGTTTTTGAAA
original cDNA sequence snippet TTTTACCCCTGAATGCAAGTTTAAAGAATCTGTTTTTGAAA
altered cDNA sequence snippet TTTTACCCCTGAATGCAAGTCTAAAGAATCTGTTTTTGAAA
wildtype AA sequence MAAAIASGLI RQKRQAREQH WDRPSASRRR SSPSKNRGLC NGNLVDIFSK VRIFGLKKRR
LRRQDPQLKG IVTRLYCRQG YYLQMHPDGA LDGTKDDSTN STLFNLIPVG LRVVAIQGVK
TGLYIAMNGE GYLYPSELFT PECKFKESVF ENYYVIYSSM LYRQQESGRA WFLGLNKEGQ
AMKGNRVKKT KPAAHFLPKP LEVAMYREPS LHDVGETVPK PGVTPSKSTS ASAIMNGGKP
VNKSKTT*
mutated AA sequence MAAAIASGLI RQKRQAREQH WDRPSASRRR SSPSKNRGLC NGNLVDIFSK VRIFGLKKRR
LRRQDPQLKG IVTRLYCRQG YYLQMHPDGA LDGTKDDSTN STLFNLIPVG LRVVAIQGVK
TGLYIAMNGE GYLYPSELFT PECKSKESVF ENYYVIYSSM LYRQQESGRA WFLGLNKEGQ
AMKGNRVKKT KPAAHFLPKP LEVAMYREPS LHDVGETVPK PGVTPSKSTS ASAIMNGGKP
VNKSKTT*
speed 1.67 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