mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 9.20414760332881e-07 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM021486)
known disease mutation: rs17934 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:116706733C>GN/A show variant in all transcripts IGV

HGNC symbol

APOA1

Ensembl transcript ID

ENST00000236850

Genbank transcript ID

NM_000039

UniProt peptide

P02647

alteration type

single base exchange

alteration region

CDS

DNA changes

c.595G>C
cDNA.961G>C
g.1934G>C

AA changes

A199P Score: 27 explain score(s)

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

199

frameshift

known variant

Reference ID: rs121912730
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17934 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM021486)

known disease mutation at this position, please check HGMD for details (HGMD ID CM021486)
known disease mutation at this position, please check HGMD for details (HGMD ID CM021486)

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
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
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.932	0
	0.02	0.007
(flanking)	2.795	0.124

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 increased	1940	wt: 0.61 / mu: 0.84	wt: TGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAG mu: TGCGCCAGCGCTTGCCCGCGCGCCTTGAGGCTCTCAAGGAG	gcgc\|GCCT

distance from splice site

267

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

199

mutated

not conserved

199

Ptroglodytes

all identical

ENSPTRG00000004316

199

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000032083

198

Ggallus

all conserved

ENSGALG00000007114

184

Trubripes

all identical

ENSTRUG00000007686

195

Drerio

not conserved

ENSDARG00000086583

213

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000003763

191

protein features

start (aa)	end (aa)	feature	details
68	267	REGION	10 X approximate tandem repeats.	lost
166	203	HELIX		lost
189	210	REPEAT	7.	lost
211	232	REPEAT	8.	might get lost (downstream of altered splice site)
212	214	TURN		might get lost (downstream of altered splice site)
215	217	STRAND		might get lost (downstream of altered splice site)
220	237	HELIX		might get lost (downstream of altered splice site)
233	243	REPEAT	9; half-length.	might get lost (downstream of altered splice site)
238	240	STRAND		might get lost (downstream of altered splice site)
243	266	HELIX		might get lost (downstream of altered splice site)
244	267	REPEAT	10.	might get lost (downstream of altered splice site)
263	263	CARBOHYD	N-linked (Glc) (glycation).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

804 / 804

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

268 / 268

position of stopcodon in wt / mu cDNA

1170 / 1170

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

367 / 367

chromosome

strand

-1

last intron/exon boundary

567

theoretical NMD boundary in CDS

150

length of CDS

804

coding sequence (CDS) position

595

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

961

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

1934

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

116706733

original gDNA sequence snippet

ACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTC

altered gDNA sequence snippet

ACGAGCTGCGCCAGCGCTTGCCCGCGCGCCTTGAGGCTCTC

original cDNA sequence snippet

ACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTC

altered cDNA sequence snippet

ACGAGCTGCGCCAGCGCTTGCCCGCGCGCCTTGAGGCTCTC

wildtype AA sequence

MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*

mutated AA sequence

MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLPA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*

speed

0.43 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