Prediction |
polymorphism |
Model: simple_aae, prob: 0.00407615224968628 (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 | ENST00000434900 |
| Genbank transcript ID | NM_001145279 |
| UniProt peptide | P35372 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.397A>G
cDNA.915A>G
g.29167A>G |
| AA changes | N133D Score: 23 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 133 |
| frameshift | no |
| known variant | Reference ID: rs1799971
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 179 | 761 | 940 |
| ExAC | 2888 | 16551 | 19439 |
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 | | PhyloP | PhastCons |
| (flanking) | 2.823 | 1 | | 2.801 | 1 | | (flanking) | 2.071 | 1 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | | effect | gDNA position | score | wt detection sequence | exon-intron border | | Acc marginally increased | 29159 | wt: 0.7097 / mu: 0.7727 (marginal change - not scored) | wt: CTGGGTCAACTTGTCCCACTTAGATGGCAACCTGTCCGACC
mu: CTGGGTCAACTTGTCCCACTTAGATGGCGACCTGTCCGACC | actt|AGAT | | Acc increased | 29160 | wt: 0.25 / mu: 0.39 | wt: TGGGTCAACTTGTCCCACTTAGATGGCAACCTGTCCGACCC
mu: TGGGTCAACTTGTCCCACTTAGATGGCGACCTGTCCGACCC | ctta|GATG | | Donor marginally increased | 29164 | wt: 0.6285 / mu: 0.6321 (marginal change - not scored) | wt: TAGATGGCAACCTGT
mu: TAGATGGCGACCTGT | GATG|gcaa |
|
| distance from splice site | 173 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 133 | G | S | W | V | N | L | S | H | L | D | G | N | L | S | D | P | C | G | P | N | R | T | D | L |
| mutated | all conserved | | 133 | G | S | W | V | N | L | S | H | L | D | G | D | L | S | D | P | C | G | P | N | R | T | D |
| Ptroglodytes | all identical | ENSPTRG00000018723 | 40 | G | S | W | V | N | L | S | H | L | D | G | N | L | S | D | P | C | G | P | N | R | T | D |
| Mmulatta | all identical | ENSMMUG00000022691 | 40 | G | S | W | V | N | L | S | H | L | D | G | N | L | S | D | P | C | G | P | N | R | T | D |
| Fcatus | no homologue | | | |
| Mmusculus | all identical | ENSMUSG00000000766 | 40 | G | S | W | L | N | L | S | H | V | D | G | N | Q | S | D | P | C | G | P | N | R | T | G |
| Ggallus | all identical | ENSGALG00000013616 | 42 | G | A | W | G | N | - | S | T | A | G | W | N | R | S | E | P | C | G | G | A | N | G | S |
| Trubripes | no homologue | | | |
| Drerio | all identical | ENSDARG00000039434 | 35 | - | - | - | - | N | S | S | I | F | C | R | N | F | S | N | S | S | G | L | - | - | - | - |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 124 | 145 | TOPO_DOM | Extracellular (Potential). | lost | | 142 | 142 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 142 | 142 | MUTAGEN | C->A,S: Abolishes ligand binding; when associated with A-219 or S-219. | might get lost (downstream of altered splice site) | | 146 | 165 | TRANSMEM | Helical; Name=3; (Potential). | might get lost (downstream of altered splice site) | | 166 | 195 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 168 | 168 | MOD_RES | Phosphotyrosine (By similarity). | might get lost (downstream of altered splice site) | | 196 | 211 | TRANSMEM | Helical; Name=4; (Potential). | might get lost (downstream of altered splice site) | | 207 | 207 | CONFLICT | M -> I (in Ref. 2; AAB60354). | might get lost (downstream of altered splice site) | | 212 | 236 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 219 | 219 | MUTAGEN | C->A,S: Abolishes ligand binding; when associated with A-142 or S-142. | might get lost (downstream of altered splice site) | | 219 | 219 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 234 | 234 | CONFLICT | L -> V (in Ref. 1; AAA20580). | might get lost (downstream of altered splice site) | | 237 | 259 | TRANSMEM | Helical; Name=5; (Potential). | might get lost (downstream of altered splice site) | | 260 | 282 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 273 | 273 | MUTAGEN | K->A: Impairs interaction with calmodulin. | might get lost (downstream of altered splice site) | | 275 | 275 | MUTAGEN | R->A: Impairs interaction with calmodulin. | might get lost (downstream of altered splice site) | | 283 | 305 | TRANSMEM | Helical; Name=6; (Potential). | might get lost (downstream of altered splice site) | | 306 | 313 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 314 | 330 | TRANSMEM | Helical; Name=7; (Potential). | might get lost (downstream of altered splice site) | | 331 | 400 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 353 | 353 | LIPID | S-palmitoyl cysteine (Potential). | might get lost (downstream of altered splice site) | | 365 | 365 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 372 | 372 | MOD_RES | Phosphothreonine (By similarity). | might get lost (downstream of altered splice site) | | 377 | 377 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 396 | 396 | MOD_RES | Phosphothreonine (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 | 1482 / 1482 |
| position (AA) of stopcodon in wt / mu AA sequence | 494 / 494 |
| position of stopcodon in wt / mu cDNA | 2000 / 2000 |
| 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 | 519 / 519 |
| chromosome | 6 |
| strand | 1 |
| last intron/exon boundary | 1962 |
| theoretical NMD boundary in CDS | 1393 |
| length of CDS | 1482 |
| coding sequence (CDS) position | 397 |
cDNA position
(for ins/del: last normal base / first normal base) | 915 |
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 | MCLHRRVPSE ETYSLDRFAQ NPPLFPPPSL PASESRMAHA PLLQRCGAAR TGFCKKQQEL
WQRRKEAAEA LGTRKVSVLL ATSHSGARPA VSTMDSSAAP TNASNCTDAL AYSSCSPAPS
PGSWVNLSHL DGNLSDPCGP NRTDLGGRDS LCPPTGSPSM ITAITIMALY SIVCVVGLFG
NFLVMYVIVR YTKMKTATNI YIFNLALADA LATSTLPFQS VNYLMGTWPF GTILCKIVIS
IDYYNMFTSI FTLCTMSVDR YIAVCHPVKA LDFRTPRNAK IINVCNWILS SAIGLPVMFM
ATTKYRQGSI DCTLTFSHPT WYWENLLKIC VFIFAFIMPV LIITVCYGLM ILRLKSVRML
SGSKEKDRNL RRITRMVLVV VAVFIVCWTP IHIYVIIKAL VTIPETTFQT VSWHFCIALG
YTNSCLNPVL YAFLDENFKR CFREFCIPTS SNIEQQNSTR IRQNTRDHPS TANTVDRTNH
QLENLEAETA PLP* |
| mutated AA sequence | MCLHRRVPSE ETYSLDRFAQ NPPLFPPPSL PASESRMAHA PLLQRCGAAR TGFCKKQQEL
WQRRKEAAEA LGTRKVSVLL ATSHSGARPA VSTMDSSAAP TNASNCTDAL AYSSCSPAPS
PGSWVNLSHL DGDLSDPCGP NRTDLGGRDS LCPPTGSPSM ITAITIMALY SIVCVVGLFG
NFLVMYVIVR YTKMKTATNI YIFNLALADA LATSTLPFQS VNYLMGTWPF GTILCKIVIS
IDYYNMFTSI FTLCTMSVDR YIAVCHPVKA LDFRTPRNAK IINVCNWILS SAIGLPVMFM
ATTKYRQGSI DCTLTFSHPT WYWENLLKIC VFIFAFIMPV LIITVCYGLM ILRLKSVRML
SGSKEKDRNL RRITRMVLVV VAVFIVCWTP IHIYVIIKAL VTIPETTFQT VSWHFCIALG
YTNSCLNPVL YAFLDENFKR CFREFCIPTS SNIEQQNSTR IRQNTRDHPS TANTVDRTNH
QLENLEAETA PLP* |
| speed | 1.05 s |
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