mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999404928 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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

ENST00000378042

Genbank transcript ID

N/A

UniProt peptide

O76090

alteration type

single base exchange

alteration region

CDS

DNA changes

c.688G>A
cDNA.1448G>A
g.10072G>A

AA changes

V230M Score: 21 explain score(s)

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

230

frameshift

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

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	10071	sequence motif lost	-	wt: ccag\|GTGT mu: ccag.ATGT
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

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

230

mutated

all conserved

230

Ptroglodytes

not conserved

ENSPTRG00000003756

290

VAEQLINPFGE

Mmulatta

not conserved

ENSMMUG00000015147

290

VAEQLINPFGE

Fcatus

all identical

ENSFCAG00000007380

331

DDDDFETNWIVDRSLQ

Mmusculus

all identical

ENSMUSG00000037418

301

DDDDFETNWIIDRNLQ

Ggallus

all identical

ENSGALG00000007217

301

DDDDFETNWLIDRNLQ

Trubripes

no homologue

Drerio

all identical

ENSDARG00000078331

301

DDDDFETNWLVDRNLQ

Dmelanogaster

all identical

FBgn0040238

303

NPFGEDDDDFEVNWMVDRNLQ

Celegans

all identical

C01B12.3

290

AEVLLNPL

Xtropicalis

all identical

ENSXETG00000006740

302

DDDFETNWLIDRNLQ

protein features

start (aa)	end (aa)	feature	details
229	249	INTRAMEM	Potential.	lost
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

688

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

1448

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

TCTATGTTGGCTGGCTGAAGGTGTCCCTGTTGGCTGTGGAT

altered cDNA sequence snippet

TCTATGTTGGCTGGCTGAAGATGTCCCTGTTGGCTGTGGAT

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 CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKM 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

0.96 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