mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999613727 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM982025)
known disease mutation: rs2731 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61724901T>AN/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

CDS

DNA changes

c.499T>A
cDNA.1259T>A
g.7609T>A

AA changes

Y167N Score: 142 explain score(s)

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

167

frameshift

known variant

Reference ID: rs28941469
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2731 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.907	1
	4.905	1
(flanking)	4.905	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
Donor gained	7613	0.38	mu: CAACGACTGGATTAG	ACGA\|ctgg
Donor gained	7605	0.98	mu: CTGTATGCCAACGAC	GTAT\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

167

mutated

not conserved

167

Ptroglodytes

all identical

ENSPTRG00000003756

227

Mmulatta

all identical

ENSMMUG00000015147

227

Fcatus

all identical

ENSFCAG00000007380

257

Mmusculus

all identical

ENSMUSG00000037418

227

Ggallus

all identical

ENSGALG00000007217

227

Trubripes

no homologue

Drerio

all identical

ENSDARG00000078331

227

Dmelanogaster

all identical

FBgn0040238

231

Celegans

all conserved

C01B12.3

227

Xtropicalis

all identical

ENSXETG00000006740

227

protein features

start (aa)	end (aa)	feature	details
92	178	TOPO_DOM	Cytoplasmic (Potential).	lost
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

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1497 / 1497

position (AA) of stopcodon in wt / mu AA sequence

499 / 499

position of stopcodon in wt / mu cDNA

2257 / 2257

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

499

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

1259

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

7609

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

61724901

original gDNA sequence snippet

AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA

altered gDNA sequence snippet

AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA

original cDNA sequence snippet

AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA

altered cDNA sequence snippet

AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA

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

MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYANDWI 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*

speed

0.99 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