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: ENST00000209873
Querying Taster for transcript #2: ENST00000394384
Querying Taster for transcript #3: ENST00000550286
MT speed 0 s - this script 4.492851 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AAASdisease_causing_automatic0.977131103965868simple_aaeaffected0Q15Ksingle base exchangers121918549show file
AAASdisease_causing_automatic0.977131103965868simple_aaeaffected0Q15Ksingle base exchangers121918549show file
AAASdisease_causing_automatic1without_aaeaffected0single base exchangers121918549show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.977131103965868 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM010147)
  • known disease mutation at this position (HGMD CM065951)
  • known disease mutation: rs5044 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:53715207G>TN/A show variant in all transcripts   IGV
HGNC symbol AAAS
Ensembl transcript ID ENST00000209873
Genbank transcript ID NM_015665
UniProt peptide Q9NRG9
alteration type single base exchange
alteration region CDS
DNA changes c.43C>A
cDNA.209C>A
g.3442C>A
AA changes Q15K Score: 53 explain score(s)
position(s) of altered AA
if AA alteration in CDS
15
frameshift no
known variant Reference ID: rs121918549
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC02828

known disease mutation: rs5044 (pathogenic for Glucocorticoid deficiency with achalasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding (1)
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding (1)
BCLAF1, Transcription Factor, BCLAF1 Transcription Factor Binding
CBP, Transcription Factor, CBP Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cjun, Transcription Factor, Cjun TF binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
ETS1, Transcription Factor, ETS1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K56ac, Histone, Histone 3 Lysine 56 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
Pbx3, Transcription Factor, Pbx3 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3671
2.9911
(flanking)-0.1340.951
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 increased3433wt: 0.8468 / mu: 0.8574 (marginal change - not scored)wt: GGTTGTTCCCTCCTCCACCGCCTCGGGGTCAAGTCACCCTA
mu: GGTTGTTCCCTCCTCCACCGCCTCGGGGTAAAGTCACCCTA
 ccgc|CTCG
Acc marginally increased3432wt: 0.8384 / mu: 0.8432 (marginal change - not scored)wt: GGGTTGTTCCCTCCTCCACCGCCTCGGGGTCAAGTCACCCT
mu: GGGTTGTTCCCTCCTCCACCGCCTCGGGGTAAAGTCACCCT
 accg|CCTC
Donor marginally increased3444wt: 0.8976 / mu: 0.9115 (marginal change - not scored)wt: GGTCAAGTCACCCTA
mu: GGTAAAGTCACCCTA
 TCAA|gtca
Donor gained34380.46mu: CCTCGGGGTAAAGTC TCGG|ggta
distance from splice site 81
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      15LGLFPPPPPRGQVTLYEHNNELVT
mutated  all conserved    15LGLFPPPPPRGKVTLYEHNNELV
Ptroglodytes  all identical  ENSPTRG00000005012  15MGLFPPPPPRGQVTLYEHNNELV
Mmulatta  all identical  ENSMMUG00000022036  15LGLFPPPPPRGQVTLYEHNNELV
Fcatus  all identical  ENSFCAG00000005881  15LGLFPPPPPRGQVTLYEHNNELV
Mmusculus  all identical  ENSMUSG00000036678  15LGLFPPPPPRGQVTLYEHNNELV
Ggallus  no alignment  ENSGALG00000013597  n/a
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000019547  15LAVFPPPLAAGHTHTLMEQHNEL-
Dmelanogaster  no alignment  FBgn0030122  n/a
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000012664  15LDLFPPPLNGDQVPLYEYNNEMV
protein features
start (aa)end (aa)featuredetails 
3333MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
122122CONFLICTS -> P (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
135135CONFLICTR -> K (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
149188REPEATWD 1.might get lost (downstream of altered splice site)
191230REPEATWD 2.might get lost (downstream of altered splice site)
243282REPEATWD 3.might get lost (downstream of altered splice site)
285324REPEATWD 4.might get lost (downstream of altered splice site)
479479CONFLICTI -> V (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
495495MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
544546MOTIFMicrobody targeting signal (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1641 / 1641
position (AA) of stopcodon in wt / mu AA sequence 547 / 547
position of stopcodon in wt / mu cDNA 1807 / 1807
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 167 / 167
chromosome 12
strand -1
last intron/exon boundary 1583
theoretical NMD boundary in CDS 1366
length of CDS 1641
coding sequence (CDS) position 43
cDNA position
(for ins/del: last normal base / first normal base)
209
gDNA position
(for ins/del: last normal base / first normal base)
3442
chromosomal position
(for ins/del: last normal base / first normal base)
53715207
original gDNA sequence snippet CTCCTCCACCGCCTCGGGGTCAAGTCACCCTATATGAGCAC
altered gDNA sequence snippet CTCCTCCACCGCCTCGGGGTAAAGTCACCCTATATGAGCAC
original cDNA sequence snippet CTCCTCCACCGCCTCGGGGTCAAGTCACCCTATATGAGCAC
altered cDNA sequence snippet CTCCTCCACCGCCTCGGGGTAAAGTCACCCTATATGAGCAC
wildtype AA sequence MCSLGLFPPP PPRGQVTLYE HNNELVTGSS YESPPPDFRG QWINLPVLQL TKDPLKTPGR
LDHGTRTAFI HHREQVWKRC INIWRDVGLF GVLNEIANSE EEVFEWVKTA SGWALALCRW
ASSLHGSLFP HLSLRSEDLI AEFAQVTNWS SCCLRVFAWH PHTNKFAVAL LDDSVRVYNA
SSTIVPSLKH RLQRNVASLA WKPLSASVLA VACQSCILIW TLDPTSLSTR PSSGCAQVLS
HPGHTPVTSL AWAPSGGRLL SASPVDAAIR VWDVSTETCV PLPWFRGGGV TNLLWSPDGS
KILATTPSAV FRVWEAQMWT CERWPTLSGR CQTGCWSPDG SRLLFTVLGE PLIYSLSFPE
RCGEGKGCVG GAKSATIVAD LSETTIQTPD GEERLGGEAH SMVWDPSGER LAVLMKGKPR
VQDGKPVILL FRTRNSPVFE LLPCGIIQGE PGAQPQLITF HPSFNKGALL SVGWSTGRIA
HIPLYFVNAQ FPRFSPVLGR AQEPPAGGGG SIHDLPLFTE TSPTSAPWDP LPGPPPVLPH
SPHSHL*
mutated AA sequence MCSLGLFPPP PPRGKVTLYE HNNELVTGSS YESPPPDFRG QWINLPVLQL TKDPLKTPGR
LDHGTRTAFI HHREQVWKRC INIWRDVGLF GVLNEIANSE EEVFEWVKTA SGWALALCRW
ASSLHGSLFP HLSLRSEDLI AEFAQVTNWS SCCLRVFAWH PHTNKFAVAL LDDSVRVYNA
SSTIVPSLKH RLQRNVASLA WKPLSASVLA VACQSCILIW TLDPTSLSTR PSSGCAQVLS
HPGHTPVTSL AWAPSGGRLL SASPVDAAIR VWDVSTETCV PLPWFRGGGV TNLLWSPDGS
KILATTPSAV FRVWEAQMWT CERWPTLSGR CQTGCWSPDG SRLLFTVLGE PLIYSLSFPE
RCGEGKGCVG GAKSATIVAD LSETTIQTPD GEERLGGEAH SMVWDPSGER LAVLMKGKPR
VQDGKPVILL FRTRNSPVFE LLPCGIIQGE PGAQPQLITF HPSFNKGALL SVGWSTGRIA
HIPLYFVNAQ FPRFSPVLGR AQEPPAGGGG SIHDLPLFTE TSPTSAPWDP LPGPPPVLPH
SPHSHL*
speed 1.34 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: 0.977131103965868 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM010147)
  • known disease mutation at this position (HGMD CM065951)
  • known disease mutation: rs5044 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:53715207G>TN/A show variant in all transcripts   IGV
HGNC symbol AAAS
Ensembl transcript ID ENST00000394384
Genbank transcript ID NM_001173466
UniProt peptide Q9NRG9
alteration type single base exchange
alteration region CDS
DNA changes c.43C>A
cDNA.174C>A
g.3442C>A
AA changes Q15K Score: 53 explain score(s)
position(s) of altered AA
if AA alteration in CDS
15
frameshift no
known variant Reference ID: rs121918549
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC02828

known disease mutation: rs5044 (pathogenic for Glucocorticoid deficiency with achalasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding (1)
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding (1)
BCLAF1, Transcription Factor, BCLAF1 Transcription Factor Binding
CBP, Transcription Factor, CBP Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cjun, Transcription Factor, Cjun TF binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
ETS1, Transcription Factor, ETS1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K56ac, Histone, Histone 3 Lysine 56 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
Pbx3, Transcription Factor, Pbx3 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3671
2.9911
(flanking)-0.1340.951
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 increased3433wt: 0.8468 / mu: 0.8574 (marginal change - not scored)wt: GGTTGTTCCCTCCTCCACCGCCTCGGGGTCAAGTCACCCTA
mu: GGTTGTTCCCTCCTCCACCGCCTCGGGGTAAAGTCACCCTA
 ccgc|CTCG
Acc marginally increased3432wt: 0.8384 / mu: 0.8432 (marginal change - not scored)wt: GGGTTGTTCCCTCCTCCACCGCCTCGGGGTCAAGTCACCCT
mu: GGGTTGTTCCCTCCTCCACCGCCTCGGGGTAAAGTCACCCT
 accg|CCTC
Donor marginally increased3444wt: 0.8976 / mu: 0.9115 (marginal change - not scored)wt: GGTCAAGTCACCCTA
mu: GGTAAAGTCACCCTA
 TCAA|gtca
Donor gained34380.46mu: CCTCGGGGTAAAGTC TCGG|ggta
distance from splice site 81
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      15LGLFPPPPPRGQVTLYEHNNELVT
mutated  all conserved    15LGLFPPPPPRGKVTLYEHNNELV
Ptroglodytes  all identical  ENSPTRG00000005012  15MGLFPPPPPRGQVTLYEHNNELV
Mmulatta  all identical  ENSMMUG00000022036  15LGLFPPPPPRGQVTLYEHNNELV
Fcatus  all identical  ENSFCAG00000005881  15LGLFPPPPPRGQVTLYEHNNELV
Mmusculus  all identical  ENSMUSG00000036678  15LGLFPPPPPRGQVTLYEHNNELV
Ggallus  no alignment  ENSGALG00000013597  n/a
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000019547  15LAVFPPPLAAGHTHTLMEQHNEL-
Dmelanogaster  no alignment  FBgn0030122  n/a
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000012664  15LDLFPPPLNGDQVPLYEYNNEMV
protein features
start (aa)end (aa)featuredetails 
3333MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
122122CONFLICTS -> P (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
135135CONFLICTR -> K (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
149188REPEATWD 1.might get lost (downstream of altered splice site)
191230REPEATWD 2.might get lost (downstream of altered splice site)
243282REPEATWD 3.might get lost (downstream of altered splice site)
285324REPEATWD 4.might get lost (downstream of altered splice site)
479479CONFLICTI -> V (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
495495MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
544546MOTIFMicrobody targeting signal (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1542 / 1542
position (AA) of stopcodon in wt / mu AA sequence 514 / 514
position of stopcodon in wt / mu cDNA 1673 / 1673
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 132 / 132
chromosome 12
strand -1
last intron/exon boundary 1449
theoretical NMD boundary in CDS 1267
length of CDS 1542
coding sequence (CDS) position 43
cDNA position
(for ins/del: last normal base / first normal base)
174
gDNA position
(for ins/del: last normal base / first normal base)
3442
chromosomal position
(for ins/del: last normal base / first normal base)
53715207
original gDNA sequence snippet CTCCTCCACCGCCTCGGGGTCAAGTCACCCTATATGAGCAC
altered gDNA sequence snippet CTCCTCCACCGCCTCGGGGTAAAGTCACCCTATATGAGCAC
original cDNA sequence snippet CTCCTCCACCGCCTCGGGGTCAAGTCACCCTATATGAGCAC
altered cDNA sequence snippet CTCCTCCACCGCCTCGGGGTAAAGTCACCCTATATGAGCAC
wildtype AA sequence MCSLGLFPPP PPRGQVTLYE HNNELVTGSS YESPPPDFRG QWINLPVLQL TKDPLKTPGR
LDHGTRTAFI HHREQVWKRC INIWRDVGLF GVLNEIANSE EEVFEWVKTA SGWALALCRW
ASSLHGSLFP HLSLRSEDLI AEFAQVTNCT IVPSLKHRLQ RNVASLAWKP LSASVLAVAC
QSCILIWTLD PTSLSTRPSS GCAQVLSHPG HTPVTSLAWA PSGGRLLSAS PVDAAIRVWD
VSTETCVPLP WFRGGGVTNL LWSPDGSKIL ATTPSAVFRV WEAQMWTCER WPTLSGRCQT
GCWSPDGSRL LFTVLGEPLI YSLSFPERCG EGKGCVGGAK SATIVADLSE TTIQTPDGEE
RLGGEAHSMV WDPSGERLAV LMKGKPRVQD GKPVILLFRT RNSPVFELLP CGIIQGEPGA
QPQLITFHPS FNKGALLSVG WSTGRIAHIP LYFVNAQFPR FSPVLGRAQE PPAGGGGSIH
DLPLFTETSP TSAPWDPLPG PPPVLPHSPH SHL*
mutated AA sequence MCSLGLFPPP PPRGKVTLYE HNNELVTGSS YESPPPDFRG QWINLPVLQL TKDPLKTPGR
LDHGTRTAFI HHREQVWKRC INIWRDVGLF GVLNEIANSE EEVFEWVKTA SGWALALCRW
ASSLHGSLFP HLSLRSEDLI AEFAQVTNCT IVPSLKHRLQ RNVASLAWKP LSASVLAVAC
QSCILIWTLD PTSLSTRPSS GCAQVLSHPG HTPVTSLAWA PSGGRLLSAS PVDAAIRVWD
VSTETCVPLP WFRGGGVTNL LWSPDGSKIL ATTPSAVFRV WEAQMWTCER WPTLSGRCQT
GCWSPDGSRL LFTVLGEPLI YSLSFPERCG EGKGCVGGAK SATIVADLSE TTIQTPDGEE
RLGGEAHSMV WDPSGERLAV LMKGKPRVQD GKPVILLFRT RNSPVFELLP CGIIQGEPGA
QPQLITFHPS FNKGALLSVG WSTGRIAHIP LYFVNAQFPR FSPVLGRAQE PPAGGGGSIH
DLPLFTETSP TSAPWDPLPG PPPVLPHSPH SHL*
speed 1.31 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 CM010147)
  • known disease mutation at this position (HGMD CM065951)
  • known disease mutation: rs5044 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:53715207G>TN/A show variant in all transcripts   IGV
HGNC symbol AAAS
Ensembl transcript ID ENST00000550286
Genbank transcript ID N/A
UniProt peptide Q9NRG9
alteration type single base exchange
alteration region intron
DNA changes g.3442C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs121918549
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC02828

known disease mutation: rs5044 (pathogenic for Glucocorticoid deficiency with achalasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065951)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding (1)
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding (1)
BCLAF1, Transcription Factor, BCLAF1 Transcription Factor Binding
CBP, Transcription Factor, CBP Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cjun, Transcription Factor, Cjun TF binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
ETS1, Transcription Factor, ETS1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K56ac, Histone, Histone 3 Lysine 56 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
Pbx3, Transcription Factor, Pbx3 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3671
2.9911
(flanking)-0.1340.951
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splice sites splice site change before start ATG (at aa -51) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased3433wt: 0.8468 / mu: 0.8574 (marginal change - not scored)wt: GGTTGTTCCCTCCTCCACCGCCTCGGGGTCAAGTCACCCTA
mu: GGTTGTTCCCTCCTCCACCGCCTCGGGGTAAAGTCACCCTA
 ccgc|CTCG
Acc marginally increased3432wt: 0.8384 / mu: 0.8432 (marginal change - not scored)wt: GGGTTGTTCCCTCCTCCACCGCCTCGGGGTCAAGTCACCCT
mu: GGGTTGTTCCCTCCTCCACCGCCTCGGGGTAAAGTCACCCT
 accg|CCTC
Donor marginally increased3444wt: 0.8976 / mu: 0.9115 (marginal change - not scored)wt: GGTCAAGTCACCCTA
mu: GGTAAAGTCACCCTA
 TCAA|gtca
Donor gained34380.46mu: CCTCGGGGTAAAGTC TCGG|ggta
distance from splice site 731
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
3333MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
122122CONFLICTS -> P (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
135135CONFLICTR -> K (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
149188REPEATWD 1.might get lost (downstream of altered splice site)
191230REPEATWD 2.might get lost (downstream of altered splice site)
243282REPEATWD 3.might get lost (downstream of altered splice site)
285324REPEATWD 4.might get lost (downstream of altered splice site)
479479CONFLICTI -> V (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
495495MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
544546MOTIFMicrobody targeting signal (Potential).might 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 355 / 355
chromosome 12
strand -1
last intron/exon boundary 1399
theoretical NMD boundary in CDS 994
length of CDS 1269
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)
3442
chromosomal position
(for ins/del: last normal base / first normal base)
53715207
original gDNA sequence snippet CTCCTCCACCGCCTCGGGGTCAAGTCACCCTATATGAGCAC
altered gDNA sequence snippet CTCCTCCACCGCCTCGGGGTAAAGTCACCCTATATGAGCAC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MKLQTQKKRL RSEDLIAEFA QVTNWSSCCL RVFAWHPHTN KFAVALLDDS VRVYNASSTI
VPSLKHRLQR NVASLAWKPL SASVLAVACQ SCILIWTLDP TSLSTRPSSG CAQVLSHPGH
TPVTSLAWAP SGGRLLSASP VDAAIRVWDV STETCVPLPW FRGGGVTNLL WSPDGSKILA
TTPSAVFRVW EAQMWTCERW PTLSGRCQTG CWSPDGSRLL FTVLGEPLIY SLSFPERCGE
GKGCVGGAKS ATIVADLSET TIQTPDGEER LGGEAHSMVW DPSGERLAVL MKGKPRVQDG
KPVILLFRTR NSPVFELLPC GIIQGEPGAQ PQLITFHPSF NKGALLSVGW STGRIAHIPL
YFVNAQFPRF SPVLGRAQEP PAGGGGSIHD LPLFTETSPT SAPWDPLPGP PPVLPHSPHS
HL*
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
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