mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999999 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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)

chr12:58025813G>CN/A show variant in all transcripts IGV

HGNC symbol

B4GALNT1

Ensembl transcript ID

ENST00000418555

Genbank transcript ID

N/A

UniProt peptide

Q00973

alteration type

single base exchange

alteration region

CDS

DNA changes

c.103C>G
cDNA.211C>G
g.1326C>G

AA changes

L35V Score: 32 explain score(s)

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

frameshift

known variant

Reference ID: rs774896

database	homozygous (C/C)	heterozygous	allele carriers
1000G	187	888	1075
ExAC	471	3094	3565

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.463	0.012
	0.035	0.003
(flanking)	-0.125	0.001

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 gained	1325	0.45	mu: CGGGACGCGCCCGGCCTCCGGGTACCTCTTGCGCCGTGGGC	ccgg\|GTAC

distance from splice site

104

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000005143

Mmulatta

not conserved

ENSMMUG00000001182

Fcatus

no alignment

ENSFCAG00000002090

n/a

Mmusculus

not conserved

ENSMUSG00000006731

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000012842

n/a

Drerio

no alignment

ENSDARG00000077352

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000006222

n/a

protein features

start (aa)	end (aa)	feature	details
26	533	TOPO_DOM	Lumenal (Potential).	lost
79	79	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
80	80	DISULFID	Interchain (with C-412).	might get lost (downstream of altered splice site)
80	80	DISULFID	Interchain (with C-412).	might get lost (downstream of altered splice site)
82	82	DISULFID	Interchain (with C-529).	might get lost (downstream of altered splice site)
82	82	DISULFID	Interchain (with C-529).	might get lost (downstream of altered splice site)
179	179	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
274	274	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
412	412	DISULFID	Interchain (with C-80).	might get lost (downstream of altered splice site)
412	412	DISULFID	Interchain (with C-80).	might get lost (downstream of altered splice site)
429	429	DISULFID		might get lost (downstream of altered splice site)
476	476	DISULFID		might get lost (downstream of altered splice site)
529	529	DISULFID	Interchain (with C-82).	might get lost (downstream of altered splice site)
529	529	DISULFID	Interchain (with C-82).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1437 / 1437

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

479 / 479

position of stopcodon in wt / mu cDNA

1545 / 1545

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

109 / 109

chromosome

strand

-1

last intron/exon boundary

1328

theoretical NMD boundary in CDS

1169

length of CDS

1437

coding sequence (CDS) position

103

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

211

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

1326

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

58025813

original gDNA sequence snippet

GGGACGCGCCCGGCCTCCGGCTACCTCTTGCGCCGTGGGCG

altered gDNA sequence snippet

GGGACGCGCCCGGCCTCCGGGTACCTCTTGCGCCGTGGGCG

original cDNA sequence snippet

GGGACGCGCCCGGCCTCCGGCTACCTCTTGCGCCGTGGGCG

altered cDNA sequence snippet

GGGACGCGCCCGGCCTCCGGGTACCTCTTGCGCCGTGGGCG

wildtype AA sequence

MWLGRRALCA LVLLLACASL GLLYASTRDA PGLRLPLAPW APPQSPRRPE LPDLAPEPRY
AHIPVRIKEQ VVGSQSPADQ LLIAPANSPL QYPLQGVEVQ PLRSILVPGL SLQAASGQEV
YQVNLTASLG TWDVAGEVTG VTLTGEGQAD LTLVSPGLDQ LNRQLQLVTY SSRSYQTNTA
DTVRFSTEGH EAAFTIRIRH PPNPRLYPPG SLPQGAQYNI SALVTIATKT FLRYDRLRAL
ITSIRRFYPT VTVVIADDSD KPERVSGPYV EHYLMPFGKG WFAGRNLAVS QVTTKYVLWV
DDDFVFTART RLERLVDVLE RTPLDLVGGA VREISGFATT YRQLLSVEPG APGLGNCLRQ
RRGFHHELVG FPGCVVTDGV VNFFLARTDK VREVGFDPRL SRVAHLEFFL DGLGSLRVGS
CSDVVVDHAS KLKLPWTSRD AGAETYARYR YPGSLDESQM AKHRLLFFKH RLQCMTSQ*

mutated AA sequence

MWLGRRALCA LVLLLACASL GLLYASTRDA PGLRVPLAPW APPQSPRRPE LPDLAPEPRY
AHIPVRIKEQ VVGSQSPADQ LLIAPANSPL QYPLQGVEVQ PLRSILVPGL SLQAASGQEV
YQVNLTASLG TWDVAGEVTG VTLTGEGQAD LTLVSPGLDQ LNRQLQLVTY SSRSYQTNTA
DTVRFSTEGH EAAFTIRIRH PPNPRLYPPG SLPQGAQYNI SALVTIATKT FLRYDRLRAL
ITSIRRFYPT VTVVIADDSD KPERVSGPYV EHYLMPFGKG WFAGRNLAVS QVTTKYVLWV
DDDFVFTART RLERLVDVLE RTPLDLVGGA VREISGFATT YRQLLSVEPG APGLGNCLRQ
RRGFHHELVG FPGCVVTDGV VNFFLARTDK VREVGFDPRL SRVAHLEFFL DGLGSLRVGS
CSDVVVDHAS KLKLPWTSRD AGAETYARYR YPGSLDESQM AKHRLLFFKH RLQCMTSQ*

speed

1.14 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