mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.997947319868686 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM064361)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:48437456C>GN/A show variant in all transcripts IGV

HGNC symbol

XYLT2

Ensembl transcript ID

ENST00000507602

Genbank transcript ID

N/A

UniProt peptide

Q9H1B5

alteration type

single base exchange

alteration region

intron

DNA changes

g.14004C>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6504649

database	homozygous (G/G)	heterozygous	allele carriers
1000G	198	861	1059
ExAC	7305	18157	25462

known disease mutation at this position, please check HGMD for details (HGMD ID CM064361)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.091	0
	1.752	0.004
(flanking)	-2.428	0

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
Donor increased	14003	wt: 0.24 / mu: 0.91	wt: GGCACACACAGCTCA mu: GGCACAGACAGCTCA	CACA\|caca
Donor gained	13998	0.38	mu: CCAGCGGCACAGACA	AGCG\|gcac

distance from splice site

2843

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
37	865	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
683	683	CARBOHYD	N-linked (GlcNAc...) (Potential).	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

7 / 7

chromosome

strand

last intron/exon boundary

1948

theoretical NMD boundary in CDS

1891

length of CDS

2031

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)

14004

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

48437456

original gDNA sequence snippet

GGAGGCTGCCCAGCGGCACACACAGCTCACAGGCCCTGCGC

altered gDNA sequence snippet

GGAGGCTGCCCAGCGGCACAGACAGCTCACAGGCCCTGCGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVASARVQKL VRRYKLAIAT ALAILLLQGL VVWSFSGLEE DEAGEKGRQR KPRPLDPGEG
SKDTDSSAGR RGSTGRRHGR WRGRAESPGV PVAKVVRAVT SRQRASRRVP PAPPPEAPGR
QNLSGAAAGE ALVGAAGFPP HGDTGSVEGA PQPTDNGFTP KCEIVGKDAL SALARASTKQ
CQQEIANVVC LHQAGSLMPK AVPRHCQLTG KMSPGIQWDE SQAQQPMDGP PVRIAYMLVV
HGRAIRQLKR LLKAVYHEQH FFYIHVDKRS DYLHREVVEL AQGYDNVRVT PWRMVTIWGG
ASLLRMYLRS MRDLLEVPGW AWDFFINLSA TDYPTRTNEE LVAFLSKNRD KNFLKSHGRD
NSRFIKKQGL DRLFHECDSH MWRLGERQIP AGIVVDGGSD WFVLTRSFVE YVVYTDDPLV
AQLRQFYTYT LLPAESFFHT VLENSLACET LVDNNLRVTN WNRKLGCKCQ YKHIVDWCGC
SPNDFKPQDF LRLQQVSRPT FFARKFESTV NQEVLEILDF HLYGSYPPGT PALKAYWENT
YDAADGPSGL SDVMLTAYTA FARLSLHHAA TAAPPMGTPL CRFEPRGLPS SVHLYFYDDH
FQGYLVTQAV QPSAQGPAET LEMWLMPQGS LKLLGRSDQA SRLQSLENRG LSMLPRLVSN
SWPQAVLPLQ PPKALG*

mutated AA sequence

N/A

speed

0.83 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