mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999516327 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM070652)
known disease mutation: rs6172 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:219525813G>CN/A show variant in all transcripts IGV

HGNC symbol

BCS1L

Ensembl transcript ID

ENST00000392109

Genbank transcript ID

NM_001257343

UniProt peptide

Q9Y276

alteration type

single base exchange

alteration region

CDS

DNA changes

c.103G>C
cDNA.369G>C
g.2327G>C

AA changes

G35R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs121908579
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6172 (pathogenic for Bjornstad syndrome with mild mitochondrial complex III deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070652)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070652)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070652)

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.47	1
	4.408	1
(flanking)	6.071	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	2322	wt: 0.4350 / mu: 0.4740 (marginal change - not scored)	wt: CACAGCCCTGGCCCTGGCCCGGAAGGGTGTCCAACTGGGCC mu: CACAGCCCTGGCCCTGGCCCGGAAGCGTGTCCAACTGGGCC	cccg\|GAAG
Donor increased	2322	wt: 0.56 / mu: 0.93	wt: GGCCCGGAAGGGTGT mu: GGCCCGGAAGCGTGT	CCCG\|gaag
Donor marginally increased	2320	wt: 0.8636 / mu: 0.9492 (marginal change - not scored)	wt: CTGGCCCGGAAGGGT mu: CTGGCCCGGAAGCGT	GGCC\|cgga

distance from splice site

152

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000006740

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026172

Ggallus

all identical

ENSGALG00000011386

Trubripes

all identical

ENSTRUG00000006343

Drerio

all identical

ENSDARG00000012295

Dmelanogaster

all identical

FBgn0032195

Celegans

not conserved

F54C9.6

Xtropicalis

all identical

ENSXETG00000013844

protein features

start (aa)	end (aa)	feature	details
16	32	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
33	419	TOPO_DOM	Mitochondrial matrix (Potential).	lost
181	181	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
230	237	NP_BIND	ATP (Potential).	might get lost (downstream of altered splice site)
394	394	CONFLICT	A -> T (in Ref. 6; CAE11877).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1260 / 1260

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

420 / 420

position of stopcodon in wt / mu cDNA

1526 / 1526

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

267 / 267

chromosome

strand

last intron/exon boundary

1274

theoretical NMD boundary in CDS

957

length of CDS

1260

coding sequence (CDS) position

103

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

369

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

2327

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

219525813

original gDNA sequence snippet

CCCTGGCCCTGGCCCGGAAGGGTGTCCAACTGGGCCTGGTG

altered gDNA sequence snippet

CCCTGGCCCTGGCCCGGAAGCGTGTCCAACTGGGCCTGGTG

original cDNA sequence snippet

CCCTGGCCCTGGCCCGGAAGGGTGTCCAACTGGGCCTGGTG

altered cDNA sequence snippet

CCCTGGCCCTGGCCCGGAAGCGTGTCCAACTGGGCCTGGTG

wildtype AA sequence

MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*

mutated AA sequence

MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKRVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*

speed

0.73 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