mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.99999989231099 (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)

chr11:130784754C>GN/A show variant in all transcripts IGV

HGNC symbol

SNX19

Ensembl transcript ID

ENST00000528555

Genbank transcript ID

N/A

UniProt peptide

Q92543

alteration type

single base exchange

alteration region

intron

DNA changes

g.1651G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3751037

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1345	968	2313
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.461	0.02
	-0.497	0
(flanking)	0.24	0

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

splice sites

splice site change before start ATG (at aa -61) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	1642	wt: 0.59 / mu: 0.69	wt: ACAACTCATCTCATTTCCTACAGCCAAATGTTCGAGGTCCC mu: ACAACTCATCTCATTTCCTACAGCCAAATCTTCGAGGTCCC	ctac\|AGCC
Donor marginally increased	1643	wt: 0.9985 / mu: 0.9990 (marginal change - not scored)	wt: CCTACAGCCAAATGT mu: CCTACAGCCAAATCT	TACA\|gcca
Donor increased	1652	wt: 0.66 / mu: 0.82	wt: AAATGTTCGAGGTCC mu: AAATCTTCGAGGTCC	ATGT\|tcga

distance from splice site

1421

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
95	272	DOMAIN	PXA.	might get lost (downstream of altered splice site)
533	663	DOMAIN	PX.	might get lost (downstream of altered splice site)
582	582	BINDING	Phosphatidylinositol 3-phosphate (By similarity).	might get lost (downstream of altered splice site)
629	629	BINDING	Phosphatidylinositol 3-phosphate (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

359 / 359

chromosome

strand

-1

last intron/exon boundary

1345

theoretical NMD boundary in CDS

936

length of CDS

1119

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)

1651

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

130784754

original gDNA sequence snippet

CTCATTTCCTACAGCCAAATGTTCGAGGTCCCCTGTTCTTA

altered gDNA sequence snippet

CTCATTTCCTACAGCCAAATCTTCGAGGTCCCCTGTTCTTA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MDSDRVEARK SLLESFLKQL CAIPEIANSE EVQEFLALNT DARIAFVKKP FMVSRIDKMV
VSAIVDTLKT AFPRSEPQSP TEELSEAETE SKPQTEGKKA SKSRLRFSSS KISPALSVTE
AQDKILYCLQ EGNVESETLS MSAMESFIEK QTKLLEMQPT KAPEKDPEQP PKGRVDSCVS
DAAVPAQDPS NSDPGTETEL ADTALDLLLL LLTEQWKWLC TENMQKFLRL IFGTLVQRWL
EVQVANLTSP QRWVQYLLLL QESIWPGGVL PKFPRPVRTQ EQKLAAEKQA LQSLMGVLPD
LVVEILGVNK CRLSWGLVLE SLQQPLINRH LIYCLGDIIL EFLDLSASVE ESAATTSASD
TPGNSKRMGV SS*

mutated AA sequence

N/A

speed

0.75 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