mutation t@sting

Prediction

disease causing

Model: without_aae, prob: 0.000279645328818828 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM033071)
known disease mutation: rs2743 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61719400T>CN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000378042

Genbank transcript ID

N/A

UniProt peptide

O76090

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.702T>C
g.2108T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121918288

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs2743 (pathogenic for Bestrophinopathy, autosomal recessive|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.977	0
	1.436	0.002
(flanking)	-0.181	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -20) | splice site change before start ATG (at aa -18) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	2112	wt: 0.33 / mu: 0.39	wt: TTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTTTAT mu: TTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTTTAT	ctgc\|TACT
Acc increased	2105	wt: 0.57 / mu: 0.66	wt: TGGCGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCC mu: TGGCGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCC	tcct\|GCTC
Acc marginally increased	2109	wt: 0.5853 / mu: 0.6336 (marginal change - not scored)	wt: GAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTT mu: GAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTT	gctc\|TGCT

distance from splice site

Kozak consensus sequence altered?

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

761 / 761

chromosome

strand

last intron/exon boundary

2239

theoretical NMD boundary in CDS

1428

length of CDS

1497

coding sequence (CDS) position

N/A

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

702

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

2108

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

61719400

original gDNA sequence snippet

CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT

altered gDNA sequence snippet

CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT

original cDNA sequence snippet

CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT

altered cDNA sequence snippet

CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT

wildtype AA sequence

MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV SLLAVDEMHQ
DLPRMEPDMY WNKPEPQPPY TAASAQFRRA SFMGSTFNIS LNKEEMEFQP NQEDEEDAHA
GIIGRFLGLQ SHDHHPPRAN SRTKLLWPKR ESLLHEGLPK NHKAAKQNVR GQEDNKAWKL
KAVDAFKSAP LYQRPGYYSA PQTPLSPTPM FFPLEPSAPS KLHSVTGIDT KDKSLKTVSS
GAKKSFELLS ESDGALMEHP EVSQVRRKTV EFNLTDMPEI PENHLKEPLE QSPTNIHTTL
KDHMDPYWAL ENRDEAHS*

mutated AA sequence

N/A

speed

0.98 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