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 CM900016)
known disease mutation: rs17917 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:116707769C>GN/A show variant in all transcripts IGV

HGNC symbol

APOA1

Ensembl transcript ID

ENST00000375329

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.898G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs28931574
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17917 (pathogenic for Familial amyloid polyneuropathy, Iowa type) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.376	1
	2.481	0.978
(flanking)	-0.486	0.024

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 marginally increased	898	wt: 0.9817 / mu: 0.9938 (marginal change - not scored)	wt: ACAGCGGCAGAGACT mu: ACAGCCGCAGAGACT	AGCG\|gcag
Donor marginally increased	901	wt: 0.7917 / mu: 0.8707 (marginal change - not scored)	wt: GCGGCAGAGACTATG mu: GCCGCAGAGACTATG	GGCA\|gaga

distance from splice site

292

Kozak consensus sequence altered?

N/A

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

133 / 133

chromosome

strand

-1

last intron/exon boundary

267

theoretical NMD boundary in CDS

length of CDS

738

coding sequence (CDS) position

N/A

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

N/A

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

898

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

116707769

original gDNA sequence snippet

TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG

altered gDNA sequence snippet

TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSGGARGFCM LKAPHSARPF FSSRSPTALQ DESCGADLGR ALPDGLKLLD NWDSVTSTFS
KLREQLGPVT QEFWDNLEKE TEGLRQEMSK DLEEVKAKVQ PYLDDFQKKW QEEMELYRQK
VEPLRAELQE GARQKLHELQ EKLSPLGEEM RDRARAHVDA LRTHLAPYSD ELRQRLAARL
EALKENGGAR LAEYHAKATE HLSTLSEKAK PALEDLRQGL LPVLESFKVS FLSALEEYTK
KLNTQ*

mutated AA sequence

N/A

speed

0.33 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