mutation t@sting

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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 CM010002)
known disease mutation: rs4980 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:44051210C>TN/A show variant in all transcripts IGV

HGNC symbol

ABCG5

Ensembl transcript ID

ENST00000543989

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.1687G>A
g.14795G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs119480069

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	18	18

known disease mutation: rs4980 (pathogenic for Sitosterolemia|Sitosterolemia 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010002)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.047	0.988
	5.775	1
(flanking)	5.775	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
Acc marginally increased	14806	wt: 0.8011 / mu: 0.8141 (marginal change - not scored)	wt: TGATTACGCGTCTCCTTCAGAATCTGATCATGGGTTTGTTC mu: TGATTACGCATCTCCTTCAGAATCTGATCATGGGTTTGTTC	caga\|ATCT

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

1707 / 1707

chromosome

strand

-1

last intron/exon boundary

2284

theoretical NMD boundary in CDS

527

length of CDS

771

coding sequence (CDS) position

N/A

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

1687

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

14795

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

44051210

original gDNA sequence snippet

TAAGCTGGCAGTGATTACGCGTCTCCTTCAGAATCTGATCA

altered gDNA sequence snippet

TAAGCTGGCAGTGATTACGCATCTCCTTCAGAATCTGATCA

original cDNA sequence snippet

TAAGCTGGCAGTGATTACGCGTCTCCTTCAGAATCTGATCA

altered cDNA sequence snippet

TAAGCTGGCAGTGATTACGCATCTCCTTCAGAATCTGATCA

wildtype AA sequence

MGLFLLFFVL RVRSNVLKGA IQDRVGLLYQ FVGATPYTGM LNAVNLFPVL RAVSDQESQD
GLYQKWQMML AYALHVLPFS VVATMIFSSV CYWTLGLHPE VARFGYFSAA LLAPHLIGEF
LTLVLLGIVQ NPNIVNSVVA LLSIAGVLVG SGFLRNIQEM PIPFKIISYF TFQKYCSEIL
VVNEFYGLNF TCGSSNVSVT TNPMCAFTQG IQFIEKTCPG ATSRFTMNFL ILYSFIPALV
ILGIVVFKIR DHLISR*

mutated AA sequence

N/A

speed

1.19 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