mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999999752847537 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:36587223G>TN/A show variant in all transcripts IGV

HGNC symbol

APOL4

Ensembl transcript ID

ENST00000404685

Genbank transcript ID

NM_145660

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.1179C>A
g.13664C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6000173

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1087	1067	2154
ExAC	17528	-2289	15239

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.475	0.001
	0.49	0.002
(flanking)	0.458	0.002

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change occurs after stopcodon (at aa 317)

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	13661	wt: 0.5388 / mu: 0.5702 (marginal change - not scored)	wt: CAAGGGGGCAAAATC mu: CAAGGGGGAAAAATC	AGGG\|ggca
Donor gained	13660	0.84	mu: ACAAGGGGGAAAAAT	AAGG\|ggga
Donor gained	13659	0.47	mu: CACAAGGGGGAAAAA	CAAG\|gggg

distance from splice site

736

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

226 / 226

chromosome

strand

-1

last intron/exon boundary

444

theoretical NMD boundary in CDS

168

length of CDS

393

coding sequence (CDS) position

N/A

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

1179

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

13664

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

36587223

original gDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered gDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

original cDNA sequence snippet

ACTGGACTTGCACAAGGGGGCAAAATCCGAGTCTGCTGAGT

altered cDNA sequence snippet

ACTGGACTTGCACAAGGGGGAAAAATCCGAGTCTGCTGAGT

wildtype AA sequence

MEGAALLKIF VVCIWVQQNH PGWTVAGQFQ EKKRFTEEVI EYFQKKVSPV HLKILLTSDE
AWKRFVRVAE LPREEADALY EALKNLTPYV AIEDKDMQQK EQQFREWFLK VSSNQMEDSG
VHRKASCHCK *

mutated AA sequence

N/A

speed

0.94 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