Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0030489120413123 (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 CM003770)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:154360797A>GN/A show variant in all transcripts   IGV
HGNC symbol OPRM1
Ensembl transcript ID ENST00000414028
Genbank transcript ID NM_001145284
UniProt peptide P35372
alteration type single base exchange
alteration region CDS
DNA changes c.118A>G
cDNA.168A>G
g.29167A>G
AA changes N40D Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 40
frameshift no
known variant Reference ID: rs1799971
databasehomozygous (G/G)heterozygousallele carriers
1000G179761940
ExAC28881655119439

known disease mutation at this position, please check HGMD for details (HGMD ID CM003770)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Nrsf, Transcription Factor, Nrsf TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8231
2.8011
(flanking)2.0711
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 increased29159wt: 0.7097 / mu: 0.7727 (marginal change - not scored)wt: CTGGGTCAACTTGTCCCACTTAGATGGCAACCTGTCCGACC
mu: CTGGGTCAACTTGTCCCACTTAGATGGCGACCTGTCCGACC		 actt|AGAT
Acc increased29160wt: 0.25 / mu: 0.39wt: TGGGTCAACTTGTCCCACTTAGATGGCAACCTGTCCGACCC
mu: TGGGTCAACTTGTCCCACTTAGATGGCGACCTGTCCGACCC		 ctta|GATG
Donor marginally increased29164wt: 0.6285 / mu: 0.6321 (marginal change - not scored)wt: TAGATGGCAACCTGT
mu: TAGATGGCGACCTGT		 GATG|gcaa
distance from splice site 168
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      40GSWVNLSHLDGNLSDPCGPNRTDL
mutated  all conserved    40GSWVNLSHLDGDLSDPCGPNRTD
Ptroglodytes  all identical  ENSPTRG00000018723  40GSWVNLSHLDGNLSDPCGPNRTD
Mmulatta  all identical  ENSMMUG00000022691  40GSWVNLSHLDGNLSDPCGPNRTD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000000766  40GSWLNLSHVDGNQSDPCGPNRTG
Ggallus  all identical  ENSGALG00000013616  42GAWGN-STAGWNRSEPCGGANGS
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000039434  35----NSSIFCRNFSNSSGL----
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
166TOPO_DOMExtracellular (Potential).lost
4040CARBOHYDN-linked (GlcNAc...) (Potential).lost
4848CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
5151CONFLICTD -> N (in Ref. 1; AAA20580).might get lost (downstream of altered splice site)
6796TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
97105TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
106123TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
109109CONFLICTI -> V (in Ref. 6; AAQ77391).might get lost (downstream of altered splice site)
124145TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
142142MUTAGENC->A,S: Abolishes ligand binding; when associated with A-219 or S-219.might get lost (downstream of altered splice site)
142142DISULFIDBy similarity.might get lost (downstream of altered splice site)
146165TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
166195TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
168168MOD_RESPhosphotyrosine (By similarity).might get lost (downstream of altered splice site)
196211TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
207207CONFLICTM -> I (in Ref. 2; AAB60354).might get lost (downstream of altered splice site)
212236TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
219219MUTAGENC->A,S: Abolishes ligand binding; when associated with A-142 or S-142.might get lost (downstream of altered splice site)
219219DISULFIDBy similarity.might get lost (downstream of altered splice site)
234234CONFLICTL -> V (in Ref. 1; AAA20580).might get lost (downstream of altered splice site)
237259TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
260282TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
273273MUTAGENK->A: Impairs interaction with calmodulin.might get lost (downstream of altered splice site)
275275MUTAGENR->A: Impairs interaction with calmodulin.might get lost (downstream of altered splice site)
283305TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
306313TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
314330TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
331400TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
353353LIPIDS-palmitoyl cysteine (Potential).might get lost (downstream of altered splice site)
365365MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
372372MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
377377MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
396396MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1212 / 1212
position (AA) of stopcodon in wt / mu AA sequence 404 / 404
position of stopcodon in wt / mu cDNA 1262 / 1262
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 51 / 51
chromosome 6
strand 1
last intron/exon boundary 1215
theoretical NMD boundary in CDS 1114
length of CDS 1212
coding sequence (CDS) position 118
cDNA position
(for ins/del: last normal base / first normal base)		 168
gDNA position
(for ins/del: last normal base / first normal base)		 29167
chromosomal position
(for ins/del: last normal base / first normal base)		 154360797
original gDNA sequence snippet ACTTGTCCCACTTAGATGGCAACCTGTCCGACCCATGCGGT
altered gDNA sequence snippet ACTTGTCCCACTTAGATGGCGACCTGTCCGACCCATGCGGT
original cDNA sequence snippet ACTTGTCCCACTTAGATGGCAACCTGTCCGACCCATGCGGT
altered cDNA sequence snippet ACTTGTCCCACTTAGATGGCGACCTGTCCGACCCATGCGGT
wildtype AA sequence MDSSAAPTNA SNCTDALAYS SCSPAPSPGS WVNLSHLDGN LSDPCGPNRT DLGGRDSLCP
PTGSPSMITA ITIMALYSIV CVVGLFGNFL VMYVIVRYTK MKTATNIYIF NLALADALAT
STLPFQSVNY LMGTWPFGTI LCKIVISIDY YNMFTSIFTL CTMSVDRYIA VCHPVKALDF
RTPRNAKIIN VCNWILSSAI GLPVMFMATT KYRQGSIDCT LTFSHPTWYW ENLLKICVFI
FAFIMPVLII TVCYGLMILR LKSVRMLSGS KEKDRNLRRI TRMVLVVVAV FIVCWTPIHI
YVIIKALVTI PETTFQTVSW HFCIALGYTN SCLNPVLYAF LDENFKRCFR EFCIPTSSNI
EQQNSTRIRQ NTRDHPSTAN TVDRTNHQGP PAKFVADQLA GSS*
mutated AA sequence MDSSAAPTNA SNCTDALAYS SCSPAPSPGS WVNLSHLDGD LSDPCGPNRT DLGGRDSLCP
PTGSPSMITA ITIMALYSIV CVVGLFGNFL VMYVIVRYTK MKTATNIYIF NLALADALAT
STLPFQSVNY LMGTWPFGTI LCKIVISIDY YNMFTSIFTL CTMSVDRYIA VCHPVKALDF
RTPRNAKIIN VCNWILSSAI GLPVMFMATT KYRQGSIDCT LTFSHPTWYW ENLLKICVFI
FAFIMPVLII TVCYGLMILR LKSVRMLSGS KEKDRNLRRI TRMVLVVVAV FIVCWTPIHI
YVIIKALVTI PETTFQTVSW HFCIALGYTN SCLNPVLYAF LDENFKRCFR EFCIPTSSNI
EQQNSTRIRQ NTRDHPSTAN TVDRTNHQGP PAKFVADQLA GSS*
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