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MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000260600
MT speed 1.45 s - this script 5.276114 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ADCY3polymorphism_automatic5.59552404411079e-14simple_aaeaffectedS107Psingle base exchangers11676272show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999944 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM122009)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:25141538A>GN/A show variant in all transcripts   IGV
HGNC symbol ADCY3
Ensembl transcript ID ENST00000260600
Genbank transcript ID NM_004036
UniProt peptide O60266
alteration type single base exchange
alteration region CDS
DNA changes c.319T>C
cDNA.1171T>C
g.1171T>C
AA changes S107P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS
107
frameshift no
known variant Reference ID: rs11676272
databasehomozygous (G/G)heterozygousallele carriers
1000G91910011920
ExAC14964283917803

known disease mutation at this position, please check HGMD for details (HGMD ID CM122009)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8540.032
0.0050.001
(flanking)-2.2340
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 increased1178wt: 0.5548 / mu: 0.6056 (marginal change - not scored)wt: CGACAAGCTGGCTTCCCTCGCCGTGGCTGGAATTGGACTGG
mu: CGACAAGCTGGCTCCCCTCGCCGTGGCTGGAATTGGACTGG
 tcgc|CGTG
Acc increased1163wt: 0.33 / mu: 0.46wt: TGTGGTCTTCTCCAGCGACAAGCTGGCTTCCCTCGCCGTGG
mu: TGTGGTCTTCTCCAGCGACAAGCTGGCTCCCCTCGCCGTGG
 acaa|GCTG
Donor increased1163wt: 0.22 / mu: 0.51wt: CGACAAGCTGGCTTC
mu: CGACAAGCTGGCTCC
 ACAA|gctg
distance from splice site 357
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      107CAVVFSSDKLASLAVAGIGLVLDI
mutated  not conserved    107CAVVFSSDKLAPLAVAGIGLVLD
Ptroglodytes  not conserved  ENSPTRG00000011718  107CAVVFSSDKLAPLAVAGIGLVLD
Mmulatta  not conserved  ENSMMUG00000009600  107CAVVFSSDKLAPLAVAGIGLLLD
Fcatus  not conserved  ENSFCAG00000003651  107CAVVYSSDKLAPLVVAGMGLLLD
Mmusculus  not conserved  ENSMUSG00000020654  107CAVVFSSDKLAPLMVAGFGLVLD
Ggallus  not conserved  ENSGALG00000016608  111CAAVYAADKLAPALAAGTGLAAH
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0023416  99-----PWDQSAPTRVINCCMLLA
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
105125TRANSMEMHelical; (Potential).lost
139159TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
173193TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
226246TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
324324METALMagnesium 2 (By similarity).might get lost (downstream of altered splice site)
324324METALMagnesium 1 (By similarity).might get lost (downstream of altered splice site)
325325METALMagnesium 2; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
368368METALMagnesium 2 (By similarity).might get lost (downstream of altered splice site)
368368METALMagnesium 1 (By similarity).might get lost (downstream of altered splice site)
381401TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
402632TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
633653TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
664684TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
708728TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
736736CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
754774TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
775795TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
833853TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
8541144TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3435 / 3435
position (AA) of stopcodon in wt / mu AA sequence 1145 / 1145
position of stopcodon in wt / mu cDNA 4287 / 4287
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 853 / 853
chromosome 2
strand -1
last intron/exon boundary 4105
theoretical NMD boundary in CDS 3202
length of CDS 3435
coding sequence (CDS) position 319
cDNA position
(for ins/del: last normal base / first normal base)
1171
gDNA position
(for ins/del: last normal base / first normal base)
1171
chromosomal position
(for ins/del: last normal base / first normal base)
25141538
original gDNA sequence snippet TCTCCAGCGACAAGCTGGCTTCCCTCGCCGTGGCTGGAATT
altered gDNA sequence snippet TCTCCAGCGACAAGCTGGCTCCCCTCGCCGTGGCTGGAATT
original cDNA sequence snippet TCTCCAGCGACAAGCTGGCTTCCCTCGCCGTGGCTGGAATT
altered cDNA sequence snippet TCTCCAGCGACAAGCTGGCTCCCCTCGCCGTGGCTGGAATT
wildtype AA sequence MPRNQGFSEP EYSAEYSAEY SVSLPSDPDR GVGRTHEISV RNSGSCLCLP RFMRLTFVPE
SLENLYQTYF KRQRHETLLV LVVFAALFDC YVVVMCAVVF SSDKLASLAV AGIGLVLDII
LFVLCKKGLL PDRVTRRVLP YVLWLLITAQ IFSYLGLNFA RAHAASDTVG WQVFFVFSFF
ITLPLSLSPI VIISVVSCVV HTLVLGVTVA QQQQEELKGM QLLREILANV FLYLCAIAVG
IMSYYMADRK HRKAFLEARQ SLEVKMNLEE QSQQQENLML SILPKHVADE MLKDMKKDES
QKDQQQFNTM YMYRHENVSI LFADIVGFTQ LSSACSAQEL VKLLNELFAR FDKLAAKYHQ
LRIKILGDCY YCICGLPDYR EDHAVCSILM GLAMVEAISY VREKTKTGVD MRVGVHTGTV
LGGVLGQKRW QYDVWSTDVT VANKMEAGGI PGRVHISQST MDCLKGEFDV EPGDGGSRCD
YLEEKGIETY LIIASKPEVK KTATQNGLNG SALPNGAPAS SKSSSPALIE TKEPNGSAHS
SGSTSEKPEE QDAQADNPSF PNPRRRLRLQ DLADRVVDAS EDEHELNQLL NEALLERESA
QVVKKRNTFL LSMRFMDPEM ETRYSVEKEK QSGAAFSCSC VVLLCTALVE ILIDPWLMTN
YVTFMVGEIL LLILTICSLA AIFPRAFPKK LVAFSTWIDR TRWARNTWAM LAIFILVMAN
VVDMLSCLQY YTGPSNATAG METEGSCLEN PKYYNYVAVL SLIATIMLVQ VSHMVKLTLM
LLVAGAVATI NLYAWRPVFD EYDHKRFREH DLPMVALEQM QGFNPGLNGT DRLPLVPSKY
SMTVMVFLMM LSFYYFSRHV EKLARTLFLW KIEVHDQKER VYEMRRWNEA LVTNMLPEHV
ARHFLGSKKR DEELYSQTYD EIGVMFASLP NFADFYTEES INNGGIECLR FLNEIISDFD
SLLDNPKFRV ITKIKTIGST YMAASGVTPD VNTNGFASSN KEDKSERERW QHLADLADFA
LAMKDTLTNI NNQSFNNFML RIGMNKGGVL AGVIGARKPH YDIWGNTVNV ASRMESTGVM
GNIQVVEETQ VILREYGFRF VRRGPIFVKG KGELLTFFLK GRDKLATFPN GPSVTLPHQV
VDNS*
mutated AA sequence MPRNQGFSEP EYSAEYSAEY SVSLPSDPDR GVGRTHEISV RNSGSCLCLP RFMRLTFVPE
SLENLYQTYF KRQRHETLLV LVVFAALFDC YVVVMCAVVF SSDKLAPLAV AGIGLVLDII
LFVLCKKGLL PDRVTRRVLP YVLWLLITAQ IFSYLGLNFA RAHAASDTVG WQVFFVFSFF
ITLPLSLSPI VIISVVSCVV HTLVLGVTVA QQQQEELKGM QLLREILANV FLYLCAIAVG
IMSYYMADRK HRKAFLEARQ SLEVKMNLEE QSQQQENLML SILPKHVADE MLKDMKKDES
QKDQQQFNTM YMYRHENVSI LFADIVGFTQ LSSACSAQEL VKLLNELFAR FDKLAAKYHQ
LRIKILGDCY YCICGLPDYR EDHAVCSILM GLAMVEAISY VREKTKTGVD MRVGVHTGTV
LGGVLGQKRW QYDVWSTDVT VANKMEAGGI PGRVHISQST MDCLKGEFDV EPGDGGSRCD
YLEEKGIETY LIIASKPEVK KTATQNGLNG SALPNGAPAS SKSSSPALIE TKEPNGSAHS
SGSTSEKPEE QDAQADNPSF PNPRRRLRLQ DLADRVVDAS EDEHELNQLL NEALLERESA
QVVKKRNTFL LSMRFMDPEM ETRYSVEKEK QSGAAFSCSC VVLLCTALVE ILIDPWLMTN
YVTFMVGEIL LLILTICSLA AIFPRAFPKK LVAFSTWIDR TRWARNTWAM LAIFILVMAN
VVDMLSCLQY YTGPSNATAG METEGSCLEN PKYYNYVAVL SLIATIMLVQ VSHMVKLTLM
LLVAGAVATI NLYAWRPVFD EYDHKRFREH DLPMVALEQM QGFNPGLNGT DRLPLVPSKY
SMTVMVFLMM LSFYYFSRHV EKLARTLFLW KIEVHDQKER VYEMRRWNEA LVTNMLPEHV
ARHFLGSKKR DEELYSQTYD EIGVMFASLP NFADFYTEES INNGGIECLR FLNEIISDFD
SLLDNPKFRV ITKIKTIGST YMAASGVTPD VNTNGFASSN KEDKSERERW QHLADLADFA
LAMKDTLTNI NNQSFNNFML RIGMNKGGVL AGVIGARKPH YDIWGNTVNV ASRMESTGVM
GNIQVVEETQ VILREYGFRF VRRGPIFVKG KGELLTFFLK GRDKLATFPN GPSVTLPHQV
VDNS*
speed 1.45 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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Problems