mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.00169526075659032 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:52675188G>TN/A show variant in all transcripts IGV

HGNC symbol

BCAS1

Ensembl transcript ID

ENST00000411563

Genbank transcript ID

N/A

UniProt peptide

O75363

alteration type

single base exchange

alteration region

intron

DNA changes

g.12117C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs394732

database	homozygous (T/T)	heterozygous	allele carriers
1000G	911	1063	1974
ExAC	14592	3583	18175

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H2AZ, Histone, Histone 2A variant Z
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.613	0.958
	-0.247	0.046
(flanking)	0.007	0.006

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

splice sites

splice site change before start ATG (at aa -49) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	12119	wt: 0.9122 / mu: 0.9585 (marginal change - not scored)	wt: TACCAGGTAGTGTAG mu: TACAAGGTAGTGTAG	CCAG\|gtag
Donor marginally increased	12122	wt: 0.9911 / mu: 0.9923 (marginal change - not scored)	wt: CAGGTAGTGTAGTAA mu: AAGGTAGTGTAGTAA	GGTA\|gtgt
Donor increased	12111	wt: 0.24 / mu: 0.31	wt: CAGAGACTTACCAGG mu: CAGAGACTTACAAGG	GAGA\|ctta
Donor marginally increased	12114	wt: 0.4592 / mu: 0.4900 (marginal change - not scored)	wt: AGACTTACCAGGTAG mu: AGACTTACAAGGTAG	ACTT\|acca
Donor marginally increased	12117	wt: 0.6190 / mu: 0.6387 (marginal change - not scored)	wt: CTTACCAGGTAGTGT mu: CTTACAAGGTAGTGT	TACC\|aggt
Donor gained	12113	0.78	mu: GAGACTTACAAGGTA	GACT\|taca

distance from splice site

11784

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
361	361	CONFLICT	G -> D (in Ref. 5; CAH18437).	might get lost (downstream of altered splice site)
552	552	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

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

209 / 209

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

495

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)

12117

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

52675188

original gDNA sequence snippet

AACCAGAAGCAGAGACTTACCAGGTAGTGTAGTAACCATTA

altered gDNA sequence snippet

AACCAGAAGCAGAGACTTACAAGGTAGTGTAGTAACCATTA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MLSRPVPGRT GDQAADSSLG SVKLDVSSNK APANKDPSES WTLPVAAGPG QDTDKTPGHA
PAQDKVLSAA RDPTLLPPET GGAGGEAPSK PKDSSFFDKF FKLDKGQEKV PGDSQQEAKR
AEHQDKVDEV PGLSGQSDDV PAGKVSVPRC IHLVLNACSG ALMG*

mutated AA sequence

N/A

speed

0.67 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