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: ENST00000302053
Querying Taster for transcript #2: ENST00000403106
MT speed 2.49 s - this script 6.62677 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGAdisease_causing_automatic1.35436628663526e-12simple_aae0E545Vsingle base exchangers121909612show file
FGAdisease_causing_automatic1.49713464860584e-12simple_aae0E545Vsingle base exchangers121909612show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 1.35436628663526e-12 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940775)
  • known disease mutation: rs16410 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:155506947T>AN/A show variant in all transcripts   IGV
HGNC symbol FGA
Ensembl transcript ID ENST00000302053
Genbank transcript ID NM_000508
UniProt peptide P02671
alteration type single base exchange
alteration region CDS
DNA changes c.1634A>T
cDNA.1713A>T
g.4972A>T
AA changes E545V Score: 121 explain score(s)
position(s) of altered AA
if AA alteration in CDS
545
frameshift no
known variant Reference ID: rs121909612
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16410 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940775)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940775)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940775)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.180
0.0720
(flanking)-0.0160
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 258
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      545SPMLGEFVSETESRGSESGIFTNT
mutated  not conserved    545VSETVSRGSESGIFTN
Ptroglodytes  all identical  ENSPTRG00000016535  545VSETESRGSESGIFTN
Mmulatta  all identical  ENSMMUG00000021303  539ASEAESMGSESGTFTN
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000028001  487EFGSKTH---SDSDILTN
Ggallus  not conserved  ENSGALG00000009266  401SHVTGAGSSHLGTGGKDK--FTD
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000020741  362--LSRDGLKITVTGGDEKSL-TS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000026093  419SSSGKKTQTSQTSSSSSSSSKVTHDVFTD
protein features
start (aa)end (aa)featuredetails 
68631COILEDBy similarity.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2601 / 2601
position (AA) of stopcodon in wt / mu AA sequence 867 / 867
position of stopcodon in wt / mu cDNA 2680 / 2680
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 80 / 80
chromosome 4
strand -1
last intron/exon boundary 1971
theoretical NMD boundary in CDS 1841
length of CDS 2601
coding sequence (CDS) position 1634
cDNA position
(for ins/del: last normal base / first normal base)
1713
gDNA position
(for ins/del: last normal base / first normal base)
4972
chromosomal position
(for ins/del: last normal base / first normal base)
155506947
original gDNA sequence snippet AGAGTTTGTCAGTGAGACTGAGTCTAGGGGCTCAGAATCTG
altered gDNA sequence snippet AGAGTTTGTCAGTGAGACTGTGTCTAGGGGCTCAGAATCTG
original cDNA sequence snippet AGAGTTTGTCAGTGAGACTGAGTCTAGGGGCTCAGAATCTG
altered cDNA sequence snippet AGAGTTTGTCAGTGAGACTGTGTCTAGGGGCTCAGAATCTG
wildtype AA sequence MFSMRIVCLV LSVVGTAWTA DSGEGDFLAE GGGVRGPRVV ERHQSACKDS DWPFCSDEDW
NYKCPSGCRM KGLIDEVNQD FTNRINKLKN SLFEYQKNNK DSHSLTTNIM EILRGDFSSA
NNRDNTYNRV SEDLRSRIEV LKRKVIEKVQ HIQLLQKNVR AQLVDMKRLE VDIDIKIRSC
RGSCSRALAR EVDLKDYEDQ QKQLEQVIAK DLLPSRDRQH LPLIKMKPVP DLVPGNFKSQ
LQKVPPEWKA LTDMPQMRME LERPGGNEIT RGGSTSYGTG SETESPRNPS SAGSWNSGSS
GPGSTGNRNP GSSGTGGTAT WKPGSSGPGS TGSWNSGSSG TGSTGNQNPG SPRPGSTGTW
NPGSSERGSA GHWTSESSVS GSTGQWHSES GSFRPDSPGS GNARPNNPDW GTFEEVSGNV
SPGTRREYHT EKLVTSKGDK ELRTGKEKVT SGSTTTTRRS CSKTVTKTVI GPDGHKEVTK
EVVTSEDGSD CPEAMDLGTL SGIGTLDGFR HRHPDEAAFF DTASTGKTFP GFFSPMLGEF
VSETESRGSE SGIFTNTKES SSHHPGIAEF PSRGKSSSYS KQFTSSTSYN RGDSTFESKS
YKMADEAGSE ADHEGTHSTK RGHAKSRPVR DCDDVLQTHP SGTQSGIFNI KLPGSSKIFS
VYCDQETSLG GWLLIQQRMD GSLNFNRTWQ DYKRGFGSLN DEGEGEFWLG NDYLHLLTQR
GSVLRVELED WAGNEAYAEY HFRVGSEAEG YALQVSSYEG TAGDALIEGS VEEGAEYTSH
NNMQFSTFDR DADQWEENCA EVYGGGWWYN NCQAANLNGI YYPGGSYDPR NNSPYEIENG
VVWVSFRGAD YSLRAVRMKI RPLVTQ*
mutated AA sequence MFSMRIVCLV LSVVGTAWTA DSGEGDFLAE GGGVRGPRVV ERHQSACKDS DWPFCSDEDW
NYKCPSGCRM KGLIDEVNQD FTNRINKLKN SLFEYQKNNK DSHSLTTNIM EILRGDFSSA
NNRDNTYNRV SEDLRSRIEV LKRKVIEKVQ HIQLLQKNVR AQLVDMKRLE VDIDIKIRSC
RGSCSRALAR EVDLKDYEDQ QKQLEQVIAK DLLPSRDRQH LPLIKMKPVP DLVPGNFKSQ
LQKVPPEWKA LTDMPQMRME LERPGGNEIT RGGSTSYGTG SETESPRNPS SAGSWNSGSS
GPGSTGNRNP GSSGTGGTAT WKPGSSGPGS TGSWNSGSSG TGSTGNQNPG SPRPGSTGTW
NPGSSERGSA GHWTSESSVS GSTGQWHSES GSFRPDSPGS GNARPNNPDW GTFEEVSGNV
SPGTRREYHT EKLVTSKGDK ELRTGKEKVT SGSTTTTRRS CSKTVTKTVI GPDGHKEVTK
EVVTSEDGSD CPEAMDLGTL SGIGTLDGFR HRHPDEAAFF DTASTGKTFP GFFSPMLGEF
VSETVSRGSE SGIFTNTKES SSHHPGIAEF PSRGKSSSYS KQFTSSTSYN RGDSTFESKS
YKMADEAGSE ADHEGTHSTK RGHAKSRPVR DCDDVLQTHP SGTQSGIFNI KLPGSSKIFS
VYCDQETSLG GWLLIQQRMD GSLNFNRTWQ DYKRGFGSLN DEGEGEFWLG NDYLHLLTQR
GSVLRVELED WAGNEAYAEY HFRVGSEAEG YALQVSSYEG TAGDALIEGS VEEGAEYTSH
NNMQFSTFDR DADQWEENCA EVYGGGWWYN NCQAANLNGI YYPGGSYDPR NNSPYEIENG
VVWVSFRGAD YSLRAVRMKI RPLVTQ*
speed 1.82 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: 1.49713464860584e-12 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940775)
  • known disease mutation: rs16410 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:155506947T>AN/A show variant in all transcripts   IGV
HGNC symbol FGA
Ensembl transcript ID ENST00000403106
Genbank transcript ID NM_021871
UniProt peptide P02671
alteration type single base exchange
alteration region CDS
DNA changes c.1634A>T
cDNA.1713A>T
g.4972A>T
AA changes E545V Score: 121 explain score(s)
position(s) of altered AA
if AA alteration in CDS
545
frameshift no
known variant Reference ID: rs121909612
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16410 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940775)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940775)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940775)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.180
0.0720
(flanking)-0.0160
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 536
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      545SPMLGEFVSETESRGSESGIFTNT
mutated  not conserved    545VSETVSRGSESGIFTN
Ptroglodytes  all identical  ENSPTRG00000016535  545VSETESRGSESGIFTN
Mmulatta  all identical  ENSMMUG00000021303  539ASEAESMGSESGTFTN
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000028001  487EFGSKTH---SDSDILTN
Ggallus  not conserved  ENSGALG00000009266  401SHVTGAGSSHLGTGGKDK--FTD
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000020741  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000026093  542TGKDCDDIRQKHSSGAKSGIFKI
protein features
start (aa)end (aa)featuredetails 
68631COILEDBy similarity.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1935 / 1935
position (AA) of stopcodon in wt / mu AA sequence 645 / 645
position of stopcodon in wt / mu cDNA 2014 / 2014
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 80 / 80
chromosome 4
strand -1
last intron/exon boundary 590
theoretical NMD boundary in CDS 460
length of CDS 1935
coding sequence (CDS) position 1634
cDNA position
(for ins/del: last normal base / first normal base)
1713
gDNA position
(for ins/del: last normal base / first normal base)
4972
chromosomal position
(for ins/del: last normal base / first normal base)
155506947
original gDNA sequence snippet AGAGTTTGTCAGTGAGACTGAGTCTAGGGGCTCAGAATCTG
altered gDNA sequence snippet AGAGTTTGTCAGTGAGACTGTGTCTAGGGGCTCAGAATCTG
original cDNA sequence snippet AGAGTTTGTCAGTGAGACTGAGTCTAGGGGCTCAGAATCTG
altered cDNA sequence snippet AGAGTTTGTCAGTGAGACTGTGTCTAGGGGCTCAGAATCTG
wildtype AA sequence MFSMRIVCLV LSVVGTAWTA DSGEGDFLAE GGGVRGPRVV ERHQSACKDS DWPFCSDEDW
NYKCPSGCRM KGLIDEVNQD FTNRINKLKN SLFEYQKNNK DSHSLTTNIM EILRGDFSSA
NNRDNTYNRV SEDLRSRIEV LKRKVIEKVQ HIQLLQKNVR AQLVDMKRLE VDIDIKIRSC
RGSCSRALAR EVDLKDYEDQ QKQLEQVIAK DLLPSRDRQH LPLIKMKPVP DLVPGNFKSQ
LQKVPPEWKA LTDMPQMRME LERPGGNEIT RGGSTSYGTG SETESPRNPS SAGSWNSGSS
GPGSTGNRNP GSSGTGGTAT WKPGSSGPGS TGSWNSGSSG TGSTGNQNPG SPRPGSTGTW
NPGSSERGSA GHWTSESSVS GSTGQWHSES GSFRPDSPGS GNARPNNPDW GTFEEVSGNV
SPGTRREYHT EKLVTSKGDK ELRTGKEKVT SGSTTTTRRS CSKTVTKTVI GPDGHKEVTK
EVVTSEDGSD CPEAMDLGTL SGIGTLDGFR HRHPDEAAFF DTASTGKTFP GFFSPMLGEF
VSETESRGSE SGIFTNTKES SSHHPGIAEF PSRGKSSSYS KQFTSSTSYN RGDSTFESKS
YKMADEAGSE ADHEGTHSTK RGHAKSRPVR GIHTSPLGKP SLSP*
mutated AA sequence MFSMRIVCLV LSVVGTAWTA DSGEGDFLAE GGGVRGPRVV ERHQSACKDS DWPFCSDEDW
NYKCPSGCRM KGLIDEVNQD FTNRINKLKN SLFEYQKNNK DSHSLTTNIM EILRGDFSSA
NNRDNTYNRV SEDLRSRIEV LKRKVIEKVQ HIQLLQKNVR AQLVDMKRLE VDIDIKIRSC
RGSCSRALAR EVDLKDYEDQ QKQLEQVIAK DLLPSRDRQH LPLIKMKPVP DLVPGNFKSQ
LQKVPPEWKA LTDMPQMRME LERPGGNEIT RGGSTSYGTG SETESPRNPS SAGSWNSGSS
GPGSTGNRNP GSSGTGGTAT WKPGSSGPGS TGSWNSGSSG TGSTGNQNPG SPRPGSTGTW
NPGSSERGSA GHWTSESSVS GSTGQWHSES GSFRPDSPGS GNARPNNPDW GTFEEVSGNV
SPGTRREYHT EKLVTSKGDK ELRTGKEKVT SGSTTTTRRS CSKTVTKTVI GPDGHKEVTK
EVVTSEDGSD CPEAMDLGTL SGIGTLDGFR HRHPDEAAFF DTASTGKTFP GFFSPMLGEF
VSETVSRGSE SGIFTNTKES SSHHPGIAEF PSRGKSSSYS KQFTSSTSYN RGDSTFESKS
YKMADEAGSE ADHEGTHSTK RGHAKSRPVR GIHTSPLGKP SLSP*
speed 0.67 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