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 CM080107)
known disease mutation: rs2742 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000435278

Genbank transcript ID

N/A

UniProt peptide

O76090

alteration type

single base exchange

alteration region

intron

DNA changes

g.10072G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121918287
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2742 (pathogenic for Bestrophinopathy, autosomal recessive) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080107)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080107)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080107)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	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	10083	wt: 0.5601 / mu: 0.5851 (marginal change - not scored)	wt: GGTGACCAGGTGTCCCTGTTGGCTGTGGATGAGATGCACCA mu: GGTGACCAGATGTCCCTGTTGGCTGTGGATGAGATGCACCA	gttg\|GCTG
Acc marginally increased	10062	wt: 0.9015 / mu: 0.9032 (marginal change - not scored)	wt: TGTGGGACTTCTTCTGTCCCTGGTGACCAGGTGTCCCTGTT mu: TGTGGGACTTCTTCTGTCCCTGGTGACCAGATGTCCCTGTT	ccct\|GGTG
Donor gained	10068	0.89	mu: GGTGACCAGATGTCC	TGAC\|caga

distance from splice site

2363

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
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

114 / 114

chromosome

strand

last intron/exon boundary

828

theoretical NMD boundary in CDS

664

length of CDS

813

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)

10072

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

61727364

original gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGGTGTCCCTGTTGGCTGTGGAT

altered gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGATGTCCCTGTTGGCTGTGGAT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQPE
QRGDGVPAQS GGRGGCSRWH HWPLPRPAVP *

mutated AA sequence

N/A

speed

0.59 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