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 CM111670)
known disease mutation at this position (HGMD CM982016)
known disease mutation: rs2734 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61719303G>AN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000301774

Genbank transcript ID

N/A

UniProt peptide

O76090

alteration type

single base exchange

alteration region

intron

DNA changes

g.2011G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs28940276
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2734 (pathogenic for Vitelliform macular dystrophy type 2|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.349	0.999
	5.982	1
(flanking)	4.939	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 -129) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	2014	wt: 0.48 / mu: 0.71	wt: AAGTGGCTAATGCCC mu: AAATGGCTAATGCCC	GTGG\|ctaa
Donor increased	2013	wt: 0.30 / mu: 0.77	wt: CAAGTGGCTAATGCC mu: CAAATGGCTAATGCC	AGTG\|gcta
Donor gained	2006	0.38	mu: CACAAGCCAAATGGC	CAAG\|ccaa
Donor gained	2007	0.35	mu: ACAAGCCAAATGGCT	AAGC\|caaa

distance from splice site

1404

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	25	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
26	46	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
47	70	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
71	91	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
92	178	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
179	199	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
200	228	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
229	249	INTRAMEM	Potential.	might get lost (downstream of altered splice site)
250	270	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
271	291	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
292	585	TOPO_DOM	Cytoplasmic (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

756 / 756

chromosome

strand

last intron/exon boundary

740

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

879

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)

2011

chromosomal position
(for ins/del: last normal base / first normal base)

61719303

original gDNA sequence snippet

CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC

altered gDNA sequence snippet

CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MEFQPNQEDE EDAHAGIIGR FLGLQSHDHH PPRANSRTKL LWPKRESLLH EGLPKNHKAA
KQNVRGQEDN KAWKLKAVDA FKSAPLYQRP GYYSAPQTPL SPTPMFFPLE PSAPSKLHSV
TGIDTKDKSL KTVSSGAKKS FELLSESDGA LMEHPEVSQV RRKTVEFNLT DMPEIPENHL
KEPLEQSPTN IHTTLKDHMD PYWALENRSV LHLNQGHCIA LCPTPASLAL SLPFLHNFLG
FHHCQSTLDL RPALAWGIYL ATFTGILGKC SGPFLTSPWY HPEDFLGPGE GR*

mutated AA sequence

N/A

speed

0.81 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