MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000311450
MT speed 0 s - this script 2.851784 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PLAC8L1	polymorphism_automatic	8.91953177983851e-13	simple_aae		affected		C11S	single base exchange	rs12187913		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999108 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:145483844A>TN/A show variant in all transcripts IGV

HGNC symbol

PLAC8L1

Ensembl transcript ID

ENST00000311450

Genbank transcript ID

NM_001029869

UniProt peptide

A1L4L8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.31T>A
cDNA.89T>A
g.89T>A

AA changes

C11S Score: 112 explain score(s)

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

frameshift

known variant

Reference ID: rs12187913

database	homozygous (T/T)	heterozygous	allele carriers
1000G	129	652	781
ExAC	4965	22103	27068

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.426	0.005
	1.143	0.005
(flanking)	-0.74	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	91	wt: 0.33 / mu: 0.38	wt: AGGTGTCCTGAGGAT mu: AGGAGTCCTGAGGAT	GTGT\|cctg
Donor gained	84	0.87	mu: CTTCTTCAGGAGTCC	TCTT\|cagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000017370

Mmulatta

not conserved

ENSMMUG00000006551

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000059455

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000069031

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

534 / 534

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

178 / 178

position of stopcodon in wt / mu cDNA

592 / 592

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

59 / 59

chromosome

strand

-1

last intron/exon boundary

452

theoretical NMD boundary in CDS

343

length of CDS

534

coding sequence (CDS) position

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

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

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

145483844

original gDNA sequence snippet

TTGGAAGTAACTTCTTCAGGTGTCCTGAGGATCTTTCCTTA

altered gDNA sequence snippet

TTGGAAGTAACTTCTTCAGGAGTCCTGAGGATCTTTCCTTA

original cDNA sequence snippet

TTGGAAGTAACTTCTTCAGGTGTCCTGAGGATCTTTCCTTA

altered cDNA sequence snippet

TTGGAAGTAACTTCTTCAGGAGTCCTGAGGATCTTTCCTTA

wildtype AA sequence

MNWFGSNFFR CPEDLSLLNI YSPLLSHMSS EDEHFISNLR GHVPASAVVK QPVRGASGRT
TITAIVQTGG GWSTGLFSVC RDRRICFCGL FCPMCLECDI ARHYGECLCW PLLPGSTFAL
RIGTRERHKI QGTLCEDWLA VHCCWAFSIC QVARELKMRT SQVYEICAVP MTKDTLV*

mutated AA sequence

MNWFGSNFFR SPEDLSLLNI YSPLLSHMSS EDEHFISNLR GHVPASAVVK QPVRGASGRT
TITAIVQTGG GWSTGLFSVC RDRRICFCGL FCPMCLECDI ARHYGECLCW PLLPGSTFAL
RIGTRERHKI QGTLCEDWLA VHCCWAFSIC QVARELKMRT SQVYEICAVP MTKDTLV*

speed

0.84 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems