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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000252699
Querying Taster for transcript #2: ENST00000390009
Querying Taster for transcript #3: ENST00000424234
MT speed 4 s - this script 8.299301 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACTN4disease_causing_automatic0.999999861138078simple_aae0K255Esingle base exchangers121908415show file
ACTN4disease_causing_automatic1without_aae0single base exchangers121908415show file
ACTN4disease_causing_automatic1without_aae0single base exchangers121908415show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999861138078 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM000497)
  • known disease mutation: rs5420 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:39200926A>GN/A show variant in all transcripts   IGV
HGNC symbol ACTN4
Ensembl transcript ID ENST00000252699
Genbank transcript ID NM_004924
UniProt peptide O43707
alteration type single base exchange
alteration region CDS
DNA changes c.763A>G
cDNA.839A>G
g.62638A>G
AA changes K255E Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS
255
frameshift no
known variant Reference ID: rs121908415
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs5420 (pathogenic for Focal segmental glomerulosclerosis 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000497)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000497)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000497)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5231
4.5731
(flanking)3.0481
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 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      255EDIVNTARPDEKAIMTYVSSFYHA
mutated  all conserved    255EDIVNTARPDEEAIMTYVSSFYH
Ptroglodytes  all identical  ENSPTRG00000010935  255EDIVNTARPDEKAIMTYVSSFYH
Mmulatta  all identical  ENSMMUG00000006429  255EDIVNTARPDEKAIMTYVSSFYH
Fcatus  all identical  ENSFCAG00000000832  201EDIVNTARPDEKAIMTYVSSFYH
Mmusculus  all identical  ENSMUSG00000054808  256EDIVNTARPDEKAIMTYVSSFYH
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009876  236EDIVNTARPDEKAIMT
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000000040  202EDIVNTARPDEKAIMTYVSSFYH
protein features
start (aa)end (aa)featuredetails 
1269DOMAINActin-binding.lost
163269DOMAINCH 2.lost
254267HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2736 / 2736
position (AA) of stopcodon in wt / mu AA sequence 912 / 912
position of stopcodon in wt / mu cDNA 2812 / 2812
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 77 / 77
chromosome 19
strand 1
last intron/exon boundary 2654
theoretical NMD boundary in CDS 2527
length of CDS 2736
coding sequence (CDS) position 763
cDNA position
(for ins/del: last normal base / first normal base)
839
gDNA position
(for ins/del: last normal base / first normal base)
62638
chromosomal position
(for ins/del: last normal base / first normal base)
39200926
original gDNA sequence snippet ACACGGCCCGGCCCGACGAGAAGGCCATAATGACCTATGTG
altered gDNA sequence snippet ACACGGCCCGGCCCGACGAGGAGGCCATAATGACCTATGTG
original cDNA sequence snippet ACACGGCCCGGCCCGACGAGAAGGCCATAATGACCTATGTG
altered cDNA sequence snippet ACACGGCCCGGCCCGACGAGGAGGCCATAATGACCTATGTG
wildtype AA sequence MVDYHAANQS YQYGPSSAGN GAGGGGSMGD YMAQEDDWDR DLLLDPAWEK QQRKTFTAWC
NSHLRKAGTQ IENIDEDFRD GLKLMLLLEV ISGERLPKPE RGKMRVHKIN NVNKALDFIA
SKGVKLVSIG AEEIVDGNAK MTLGMIWTII LRFAIQDISV EETSAKEGLL LWCQRKTAPY
KNVNVQNFHI SWKDGLAFNA LIHRHRPELI EYDKLRKDDP VTNLNNAFEV AEKYLDIPKM
LDAEDIVNTA RPDEKAIMTY VSSFYHAFSG AQKAETAANR ICKVLAVNQE NEHLMEDYEK
LASDLLEWIR RTIPWLEDRV PQKTIQEMQQ KLEDFRDYRR VHKPPKVQEK CQLEINFNTL
QTKLRLSNRP AFMPSEGKMV SDINNGWQHL EQAEKGYEEW LLNEIRRLER LDHLAEKFRQ
KASIHEAWTD GKEAMLKHRD YETATLSDIK ALIRKHEAFE SDLAAHQDRV EQIAAIAQEL
NELDYYDSHN VNTRCQKICD QWDALGSLTH SRREALEKTE KQLEAIDQLH LEYAKRAAPF
NNWMESAMED LQDMFIVHTI EEIEGLISAH DQFKSTLPDA DREREAILAI HKEAQRIAES
NHIKLSGSNP YTTVTPQIIN SKWEKVQQLV PKRDHALLEE QSKQQSNEHL RRQFASQANV
VGPWIQTKME EIGRISIEMN GTLEDQLSHL KQYERSIVDY KPNLDLLEQQ HQLIQEALIF
DNKHTNYTME HIRVGWEQLL TTIARTINEV ENQILTRDAK GISQEQMQEF RASFNHFDKD
HGGALGPEEF KACLISLGYD VENDRQGEAE FNRIMSLVDP NHSGLVTFQA FIDFMSRETT
DTDTADQVIA SFKVLAGDKN FITAEELRRE LPPDQAEYCI ARMAPYQGPD AVPGALDYKS
FSTALYGESD L*
mutated AA sequence MVDYHAANQS YQYGPSSAGN GAGGGGSMGD YMAQEDDWDR DLLLDPAWEK QQRKTFTAWC
NSHLRKAGTQ IENIDEDFRD GLKLMLLLEV ISGERLPKPE RGKMRVHKIN NVNKALDFIA
SKGVKLVSIG AEEIVDGNAK MTLGMIWTII LRFAIQDISV EETSAKEGLL LWCQRKTAPY
KNVNVQNFHI SWKDGLAFNA LIHRHRPELI EYDKLRKDDP VTNLNNAFEV AEKYLDIPKM
LDAEDIVNTA RPDEEAIMTY VSSFYHAFSG AQKAETAANR ICKVLAVNQE NEHLMEDYEK
LASDLLEWIR RTIPWLEDRV PQKTIQEMQQ KLEDFRDYRR VHKPPKVQEK CQLEINFNTL
QTKLRLSNRP AFMPSEGKMV SDINNGWQHL EQAEKGYEEW LLNEIRRLER LDHLAEKFRQ
KASIHEAWTD GKEAMLKHRD YETATLSDIK ALIRKHEAFE SDLAAHQDRV EQIAAIAQEL
NELDYYDSHN VNTRCQKICD QWDALGSLTH SRREALEKTE KQLEAIDQLH LEYAKRAAPF
NNWMESAMED LQDMFIVHTI EEIEGLISAH DQFKSTLPDA DREREAILAI HKEAQRIAES
NHIKLSGSNP YTTVTPQIIN SKWEKVQQLV PKRDHALLEE QSKQQSNEHL RRQFASQANV
VGPWIQTKME EIGRISIEMN GTLEDQLSHL KQYERSIVDY KPNLDLLEQQ HQLIQEALIF
DNKHTNYTME HIRVGWEQLL TTIARTINEV ENQILTRDAK GISQEQMQEF RASFNHFDKD
HGGALGPEEF KACLISLGYD VENDRQGEAE FNRIMSLVDP NHSGLVTFQA FIDFMSRETT
DTDTADQVIA SFKVLAGDKN FITAEELRRE LPPDQAEYCI ARMAPYQGPD AVPGALDYKS
FSTALYGESD L*
speed 1.63 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM000497)
  • known disease mutation: rs5420 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:39200926A>GN/A show variant in all transcripts   IGV
HGNC symbol ACTN4
Ensembl transcript ID ENST00000390009
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.62638A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs121908415
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs5420 (pathogenic for Focal segmental glomerulosclerosis 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000497)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000497)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000497)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5231
4.5731
(flanking)3.0481
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 4183
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 9 / 9
chromosome 19
strand 1
last intron/exon boundary 1929
theoretical NMD boundary in CDS 1870
length of CDS 2079
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
62638
chromosomal position
(for ins/del: last normal base / first normal base)
39200926
original gDNA sequence snippet ACACGGCCCGGCCCGACGAGAAGGCCATAATGACCTATGTG
altered gDNA sequence snippet ACACGGCCCGGCCCGACGAGGAGGCCATAATGACCTATGTG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVDYHAANQS YQYGPSSAGN GAGGGGSMGD YMAQEDDWDR DLLLDPAWEK QQRKAETAAN
RICKVLAVNQ ENEHLMEDYE KLASDLLEWI RRTIPWLEDR VPQKTIQEMQ QKLEDFRDYR
RVHKPPKVQE KCQLEINFNT LQTKLRLSNR PAFMPSEGKM VSDINNGWQH LEQAEKGYEE
WLLNEIRRLE RLDHLAEKFR QKASIHEAWT DGKEAMLKHR DYETATLSDI KALIRKHEAF
ESDLAAHQDR VEQIAAIAQE LNELDYYDSH NVNTRCQKIC DQWDALGSLT HSRREALEKT
EKQLEAIDQL HLEYAKRAAP FNNWMESAME DLQDMFIVHT IEEIEGLISA HDQFKSTLPD
ADREREAILA IHKEAQRIAE SNHIKLSGSN PYTTVTPQII NSKWEKVQQL VPKRDHALLE
EQSKQQSNEH LRRQFASQAN VVGPWIQTKM EEIGRISIEM NGTLEDQLSH LKQYERSIVD
YKPNLDLLEQ QHQLIQEALI FDNKHTNYTM EHIRVGWEQL LTTIARTINE VENQILTRDA
KGISQEQMQE FRASFNHFDK DHGGALGPEE FKACLISLGY DVENDRQGEA EFNRIMSLVD
PNHSGLVTFQ AFIDFMSRET TDTDTADQVI ASFKVLAGDK NFITAEELRR ELPPDQAEYC
IARMAPYQGP DAVPGALDYK SFSTALYGES DL*
mutated AA sequence N/A
speed 1.09 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM000497)
  • known disease mutation: rs5420 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:39200926A>GN/A show variant in all transcripts   IGV
HGNC symbol ACTN4
Ensembl transcript ID ENST00000424234
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.62638A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs121908415
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs5420 (pathogenic for Focal segmental glomerulosclerosis 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000497)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000497)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000497)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5231
4.5731
(flanking)3.0481
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 7965
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 60 / 60
chromosome 19
strand 1
last intron/exon boundary 1467
theoretical NMD boundary in CDS 1357
length of CDS 1566
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
62638
chromosomal position
(for ins/del: last normal base / first normal base)
39200926
original gDNA sequence snippet ACACGGCCCGGCCCGACGAGAAGGCCATAATGACCTATGTG
altered gDNA sequence snippet ACACGGCCCGGCCCGACGAGGAGGCCATAATGACCTATGTG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVDYHAANQS YQYGPSSAGN GAGGGGSMGD YMAQEDDWDR DLLLDPAWEK QQRKTFTAWC
NSHLRKAGTQ IENIDEDFRD GLKLMLLLEV HELDYYDSHN VNTRCQKICD QWDALGSLTH
SRREALEKTE KQLEAIDQLH LEYAKRAAPF NNWMESAMED LQDMFIVHTI EEIEGLISAH
DQFKSTLPDA DREREAILAI HKEAQRIAES NHIKLSGSNP YTTVTPQIIN SKWEKVQQLV
PKRDHALLEE QSKQQSNEHL RRQFASQANV VGPWIQTKME EIGRISIEMN GTLEDQLSHL
KQYERSIVDY KPNLDLLEQQ HQLIQEALIF DNKHTNYTME HIRVGWEQLL TTIARTINEV
ENQILTRDAK GISQEQMQEF RASFNHFDKD HGGALGPEEF KACLISLGYD VENDRQGEAE
FNRIMSLVDP NHSGLVTFQA FIDFMSRETT DTDTADQVIA SFKVLAGDKN FITAEELRRE
LPPDQAEYCI ARMAPYQGPD AVPGALDYKS FSTALYGESD L*
mutated AA sequence N/A
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