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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: ENST00000242592
Querying Taster for transcript #2: ENST00000411593
MT speed 2.12 s - this script 6.358188 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACADSdisease_causing0.999999999970165simple_aaeaffectedA192Vsingle base exchangers28940874show file
ACADSdisease_causing1without_aaeaffectedsingle base exchangers28940874show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999970165      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM010006)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:121175742C>TN/A show variant in all transcripts   IGV
HGNC symbol ACADS
Ensembl transcript ID ENST00000242592
Genbank transcript ID NM_000017
UniProt peptide P16219
alteration type single base exchange
alteration region CDS
DNA changes c.575C>T
cDNA.726C>T
g.12205C>T
AA changes A192V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 192
frameshift no
known variant Reference ID: rs28940874
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC055

known disease mutation at this position, please check HGMD for details (HGMD ID CM010006)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010006)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010006)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6561
5.6561
(flanking)0.070.995
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased12198wt: 0.68 / mu: 0.82wt: ATGCCTGGGAGGCTT
mu: ATGCCTGGGAGGTTT		 GCCT|ggga
distance from splice site 50
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      192GTKAWITNAWEASAAVVFASTDRA
mutated  not conserved    192GTKAWITNAWEVSAAVVFASTDR
Ptroglodytes  all identical  ENSPTRG00000005547  192GTKAWITNAWEASAAVVFASTDR
Mmulatta  all identical  ENSMMUG00000020648  192GTKAWITNAWEASAAVVFASTDR
Fcatus  all identical  ENSFCAG00000002402  122EASATVVFASTDR
Mmusculus  all identical  ENSMUSG00000029545  192GTKAWITNSWEASATVVFASTDR
Ggallus  all identical  ENSGALG00000007072  196TKAWITNAWDASATVVFATTDK
Trubripes  all identical  ENSTRUG00000018610  192ASATIVFATTDK
Drerio  all identical  ENSDARG00000030781  204GTKAWITNSWDASATVVFATTD
Dmelanogaster  all identical  FBgn0038742  185AWITNAFEAEAAIVFATTNK
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000012275  189TNAWDASAAVVLATTDK
protein features
start (aa)end (aa)featuredetails 
188191TURNmight get lost (downstream of altered splice site)
193200STRANDmight get lost (downstream of altered splice site)
203205STRANDmight get lost (downstream of altered splice site)
210218STRANDmight get lost (downstream of altered splice site)
222224STRANDmight get lost (downstream of altered splice site)
230232STRANDmight get lost (downstream of altered splice site)
238249STRANDmight get lost (downstream of altered splice site)
250252HELIXmight get lost (downstream of altered splice site)
253256STRANDmight get lost (downstream of altered splice site)
260296HELIXmight get lost (downstream of altered splice site)
269272REGIONSubstrate binding.might get lost (downstream of altered splice site)
297297BINDINGFAD; shared with dimeric partner.might get lost (downstream of altered splice site)
304306HELIXmight get lost (downstream of altered splice site)
308308BINDINGFAD.might get lost (downstream of altered splice site)
308336HELIXmight get lost (downstream of altered splice site)
342367HELIXmight get lost (downstream of altered splice site)
365369NP_BINDFAD; shared with dimeric partner.might get lost (downstream of altered splice site)
368372HELIXmight get lost (downstream of altered splice site)
378388HELIXmight get lost (downstream of altered splice site)
389392TURNmight get lost (downstream of altered splice site)
392392ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
393393BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
394396NP_BINDFAD.might get lost (downstream of altered splice site)
395411HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1239 / 1239
position (AA) of stopcodon in wt / mu AA sequence 413 / 413
position of stopcodon in wt / mu cDNA 1390 / 1390
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 152 / 152
chromosome 12
strand 1
last intron/exon boundary 1238
theoretical NMD boundary in CDS 1036
length of CDS 1239
coding sequence (CDS) position 575
cDNA position
(for ins/del: last normal base / first normal base)		 726
gDNA position
(for ins/del: last normal base / first normal base)		 12205
chromosomal position
(for ins/del: last normal base / first normal base)		 121175742
original gDNA sequence snippet GATCACCAATGCCTGGGAGGCTTCGGCTGCCGTGGTCTTTG
altered gDNA sequence snippet GATCACCAATGCCTGGGAGGTTTCGGCTGCCGTGGTCTTTG
original cDNA sequence snippet GATCACCAATGCCTGGGAGGCTTCGGCTGCCGTGGTCTTTG
altered cDNA sequence snippet GATCACCAATGCCTGGGAGGTTTCGGCTGCCGTGGTCTTTG
wildtype AA sequence MAAALLARAS GPARRALCPR AWRQLHTIYQ SVELPETHQM LLQTCRDFAE KELFPIAAQV
DKEHLFPAAQ VKKMGGLGLL AMDVPEELGG AGLDYLAYAI AMEEISRGCA STGVIMSVNN
SLYLGPILKF GSKEQKQAWV TPFTSGDKIG CFALSEPGNG SDAGAASTTA RAEGDSWVLN
GTKAWITNAW EASAAVVFAS TDRALQNKGI SAFLVPMPTP GLTLGKKEDK LGIRGSSTAN
LIFEDCRIPK DSILGEPGMG FKIAMQTLDM GRIGIASQAL GIAQTALDCA VNYAENRMAF
GAPLTKLQVI QFKLADMALA LESARLLTWR AAMLKDNKKP FIKEAAMAKL AASEAATAIS
HQAIQILGGM GYVTEMPAER HYRDARITEI YEGTSEIQRL VIAGHLLRSY RS*
mutated AA sequence MAAALLARAS GPARRALCPR AWRQLHTIYQ SVELPETHQM LLQTCRDFAE KELFPIAAQV
DKEHLFPAAQ VKKMGGLGLL AMDVPEELGG AGLDYLAYAI AMEEISRGCA STGVIMSVNN
SLYLGPILKF GSKEQKQAWV TPFTSGDKIG CFALSEPGNG SDAGAASTTA RAEGDSWVLN
GTKAWITNAW EVSAAVVFAS TDRALQNKGI SAFLVPMPTP GLTLGKKEDK LGIRGSSTAN
LIFEDCRIPK DSILGEPGMG FKIAMQTLDM GRIGIASQAL GIAQTALDCA VNYAENRMAF
GAPLTKLQVI QFKLADMALA LESARLLTWR AAMLKDNKKP FIKEAAMAKL AASEAATAIS
HQAIQILGGM GYVTEMPAER HYRDARITEI YEGTSEIQRL VIAGHLLRSY RS*
speed 1.12 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      (explain)
Summary
  • known disease mutation at this position (HGMD CM010006)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:121175742C>TN/A show variant in all transcripts   IGV
HGNC symbol ACADS
Ensembl transcript ID ENST00000411593
Genbank transcript ID N/A
UniProt peptide P16219
alteration type single base exchange
alteration region intron
DNA changes g.12205C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28940874
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC055

known disease mutation at this position, please check HGMD for details (HGMD ID CM010006)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010006)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010006)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6561
5.6561
(flanking)0.070.995
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased12198wt: 0.68 / mu: 0.82wt: ATGCCTGGGAGGCTT
mu: ATGCCTGGGAGGTTT		 GCCT|ggga
distance from splice site 110
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
152161NP_BINDFAD.might get lost (downstream of altered splice site)
159162STRANDmight get lost (downstream of altered splice site)
161161BINDINGSubstrate; via carbonyl oxygen.might get lost (downstream of altered splice site)
163165HELIXmight get lost (downstream of altered splice site)
169173STRANDmight get lost (downstream of altered splice site)
176187STRANDmight get lost (downstream of altered splice site)
185187NP_BINDFAD.might get lost (downstream of altered splice site)
188191TURNmight get lost (downstream of altered splice site)
193200STRANDmight get lost (downstream of altered splice site)
203205STRANDmight get lost (downstream of altered splice site)
210218STRANDmight get lost (downstream of altered splice site)
222224STRANDmight get lost (downstream of altered splice site)
230232STRANDmight get lost (downstream of altered splice site)
238249STRANDmight get lost (downstream of altered splice site)
250252HELIXmight get lost (downstream of altered splice site)
253256STRANDmight get lost (downstream of altered splice site)
260296HELIXmight get lost (downstream of altered splice site)
269272REGIONSubstrate binding.might get lost (downstream of altered splice site)
297297BINDINGFAD; shared with dimeric partner.might get lost (downstream of altered splice site)
304306HELIXmight get lost (downstream of altered splice site)
308308BINDINGFAD.might get lost (downstream of altered splice site)
308336HELIXmight get lost (downstream of altered splice site)
342367HELIXmight get lost (downstream of altered splice site)
365369NP_BINDFAD; shared with dimeric partner.might get lost (downstream of altered splice site)
368372HELIXmight get lost (downstream of altered splice site)
378388HELIXmight get lost (downstream of altered splice site)
389392TURNmight get lost (downstream of altered splice site)
392392ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
393393BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
394396NP_BINDFAD.might get lost (downstream of altered splice site)
395411HELIXmight get lost (downstream of altered splice site)
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 26 / 26
chromosome 12
strand 1
last intron/exon boundary 1100
theoretical NMD boundary in CDS 1024
length of CDS 1227
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)		 12205
chromosomal position
(for ins/del: last normal base / first normal base)		 121175742
original gDNA sequence snippet GATCACCAATGCCTGGGAGGCTTCGGCTGCCGTGGTCTTTG
altered gDNA sequence snippet GATCACCAATGCCTGGGAGGTTTCGGCTGCCGTGGTCTTTG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MAAALLARAS GPARRALCPR AWRQLHTIYQ SVELPETHQM LLQTCRDFAE KELFPIAAQV
DKEHLFPAAQ VKKMGGLGLL AMDVPEELGG AGLDYLAYAI AMEEISRGCA STGVIMSVNN
SLYLGPILKF GSKEQKQAWV TPFTSGDKIG CFALSEPGPS LLGPTGPIFA LGQVGCPCPS
SAATEACTFP RSRQRVSRPE LLREGISAFL VPMPTPGLTL GKKEDKLGIR GSSTANLIFE
DCRIPKDSIL GEPGMGFKIA MQTLDMGRIG IASQALGIAQ TALDCAVNYA ENRMAFGAPL
TKLQVIQFKL ADMALALESA RLLTWRAAML KDNKKPFIKE AAMAKLAASE AATAISHQAI
QILGGMGYVT EMPAERHYRD ARITEIYEGT SEIQRLVIAG HLLRSYRS*
mutated AA sequence N/A
speed 1.00 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