mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.0703963021481221 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:3561396C>TN/A show variant in all transcripts IGV

HGNC symbol

CTNS

Ensembl transcript ID

ENST00000046640

Genbank transcript ID

NM_004937

UniProt peptide

O60931

alteration type

single base exchange

alteration region

CDS

DNA changes

c.779C>T
cDNA.1372C>T
g.21635C>T

AA changes

T260I Score: 89 explain score(s)

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

260

frameshift

known variant

Reference ID: rs161400

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1769	560	2329
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.977	0.99
	2.394	1
(flanking)	3.715	1

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

260

mutated

not conserved

260

Ptroglodytes

all identical

ENSPTRG00000008572

235

Mmulatta

all identical

ENSMMUG00000023389

260

Fcatus

all identical

ENSFCAG00000007923

260

Mmusculus

all identical

ENSMUSG00000005949

260

Ggallus

not conserved

ENSGALG00000004628

271

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000008890

265

Dmelanogaster

not conserved

FBgn0039045

265

Celegans

not conserved

C41C4.7

262

Xtropicalis

not conserved

ENSXETG00000005795

270

protein features

start (aa)	end (aa)	feature	details
259	261	TOPO_DOM	Lumenal (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1104 / 1104

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

368 / 368

position of stopcodon in wt / mu cDNA

1697 / 1697

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

594 / 594

chromosome

strand

last intron/exon boundary

1564

theoretical NMD boundary in CDS

920

length of CDS

1104

coding sequence (CDS) position

779

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

1372

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

21635

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

3561396

original gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered gDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

original cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGACCACGTGGCTGCAGTTTCTCT

altered cDNA sequence snippet

CGTGGCTGCAGTGGGAGTGATCACGTGGCTGCAGTTTCTCT

wildtype AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVT TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGYDQLN*

mutated AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVI TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGYDQLN*

speed

1.19 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