mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 1.58720117925414e-23 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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

ENST00000520708

Genbank transcript ID

N/A

UniProt peptide

P35372

alteration type

single base exchange

alteration region

intron

DNA changes

g.29167A>G

AA changes

N/A

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

N/A

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

splice site change before start ATG (at aa -2) |

effect	gDNA position	score	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

28644

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	66	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
9	9	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
12	12	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
26	26	CONFLICT	P -> L (in Ref. 10; BAG36624).	might get lost (downstream of altered splice site)
33	33	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
40	40	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
48	48	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
51	51	CONFLICT	D -> N (in Ref. 1; AAA20580).	might get lost (downstream of altered splice site)
67	96	TRANSMEM	Helical; Name=1; (Potential).	might get lost (downstream of altered splice site)
97	105	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
106	123	TRANSMEM	Helical; Name=2; (Potential).	might get lost (downstream of altered splice site)
109	109	CONFLICT	I -> V (in Ref. 6; AAQ77391).	might get lost (downstream of altered splice site)
124	145	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
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

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

529 / 529

chromosome

strand

last intron/exon boundary

1393

theoretical NMD boundary in CDS

814

length of CDS

903

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)

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

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

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 TVDRTNHQLE NLEAETAPLP
*

mutated AA sequence

N/A

speed

0.89 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