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 CM001378)
known disease mutation: rs2738 (pathogenic)

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

ENST00000378042

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.720G>A
g.2126G>A

AA changes

N/A

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

N/A

frameshift

N/A

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?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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)

720

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

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

0.76 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