mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.958095929524351 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM001378)
known disease mutation: rs2738 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61719418G>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

CDS

DNA changes

c.140G>A
cDNA.253G>A
g.2126G>A

AA changes

R47H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs28940278

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

known disease mutation: rs2738 (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 CM001378)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001378)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001378)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.914	1
	4.354	0.999
(flanking)	0.066	0.084

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	2130	wt: 0.4583 / mu: 0.4755 (marginal change - not scored)	wt: TGCTACTACATCATCCGCTTTATTTATAGGTAAAGCTGGCA mu: TGCTACTACATCATCCACTTTATTTATAGGTAAAGCTGGCA	cttt\|ATTT
Acc marginally increased	2132	wt: 0.7968 / mu: 0.8027 (marginal change - not scored)	wt: CTACTACATCATCCGCTTTATTTATAGGTAAAGCTGGCAGG mu: CTACTACATCATCCACTTTATTTATAGGTAAAGCTGGCAGG	ttat\|TTAT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000003756

Mmulatta

all identical

ENSMMUG00000015147

Fcatus

no alignment

ENSFCAG00000007380

n/a

Mmusculus

all identical

ENSMUSG00000037418

Ggallus

not conserved

ENSGALG00000007217

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000078331

Dmelanogaster

not conserved

FBgn0040238

Celegans

not conserved

C01B12.3

Xtropicalis

not conserved

ENSXETG00000006740

protein features

start (aa)	end (aa)	feature	details
47	70	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

813 / 813

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

271 / 271

position of stopcodon in wt / mu cDNA

926 / 926

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

140

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

253

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

2126

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

61719418

original gDNA sequence snippet

GCTCTGCTACTACATCATCCGCTTTATTTATAGGTAAAGCT

altered gDNA sequence snippet

GCTCTGCTACTACATCATCCACTTTATTTATAGGTAAAGCT

original cDNA sequence snippet

GCTCTGCTACTACATCATCCGCTTTATTTATAGGCTGGCCC

altered cDNA sequence snippet

GCTCTGCTACTACATCATCCACTTTATTTATAGGCTGGCCC

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

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

speed

0.55 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