MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000408973
MT speed 0 s - this script 2.268717 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LCNL1	polymorphism_automatic	3.44369096605401e-06	simple_aae				A68T	single base exchange	rs17578859		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999996556309034 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:139879170G>AN/A show variant in all transcripts IGV

HGNC symbol

LCNL1

Ensembl transcript ID

ENST00000408973

Genbank transcript ID

NM_207510

UniProt peptide

Q6ZST4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.202G>A
cDNA.796G>A
g.2815G>A

AA changes

A68T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs17578859

database	homozygous (A/A)	heterozygous	allele carriers
1000G	153	847	1000
ExAC	4014	20145	24159

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.563	0.666
	0.42	0.605
(flanking)	-0.08	0.096

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 marginally increased	2813	wt: 0.7271 / mu: 0.7283 (marginal change - not scored)	wt: GGCTCTCGCTCCTCCAGCCATGGCCCTGAGTGACATCCGAG mu: GGCTCTCGCTCCTCCAGCCATGACCCTGAGTGACATCCGAG	ccat\|GGCC
Acc marginally increased	2821	wt: 0.5721 / mu: 0.6212 (marginal change - not scored)	wt: CTCCTCCAGCCATGGCCCTGAGTGACATCCGAGTGGCCTTC mu: CTCCTCCAGCCATGACCCTGAGTGACATCCGAGTGGCCTTC	ctga\|GTGA
Acc marginally increased	2812	wt: 0.6121 / mu: 0.6595 (marginal change - not scored)	wt: CGGCTCTCGCTCCTCCAGCCATGGCCCTGAGTGACATCCGA mu: CGGCTCTCGCTCCTCCAGCCATGACCCTGAGTGACATCCGA	gcca\|TGGC
Donor marginally increased	2816	wt: 0.9598 / mu: 0.9653 (marginal change - not scored)	wt: CATGGCCCTGAGTGA mu: CATGACCCTGAGTGA	TGGC\|cctg

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

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000009705

102

TYFSR

Drerio

not conserved

ENSDARG00000069439

101

FNYY

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

495 / 495

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

165 / 165

position of stopcodon in wt / mu cDNA

1089 / 1089

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

595 / 595

chromosome

strand

last intron/exon boundary

791

theoretical NMD boundary in CDS

146

length of CDS

495

coding sequence (CDS) position

202

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

796

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

2815

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

139879170

original gDNA sequence snippet

CTCTCGCTCCTCCAGCCATGGCCCTGAGTGACATCCGAGTG

altered gDNA sequence snippet

CTCTCGCTCCTCCAGCCATGACCCTGAGTGACATCCGAGTG

original cDNA sequence snippet

AGTTCAGCAACCCAGCCATGGCCCTGAGTGACATCCGAGTG

altered cDNA sequence snippet

AGTTCAGCAACCCAGCCATGACCCTGAGTGACATCCGAGTG

wildtype AA sequence

MVGVVSDDQD FLDSKDTMKM AVVLVTPLGN GDLALKFGYP TPHGGCQKMD TTFTEGAVPG
QFSNPAMALS DIRVAFSDYQ HFALLYLEMR KGGLRNQWLQ LYGGRAAGRR PRHPRFGSGM
SPLCLHQPFL HAEGGTAGSW CLWPRVPAPP CPSLPLFAPP APSL*

mutated AA sequence

MVGVVSDDQD FLDSKDTMKM AVVLVTPLGN GDLALKFGYP TPHGGCQKMD TTFTEGAVPG
QFSNPAMTLS DIRVAFSDYQ HFALLYLEMR KGGLRNQWLQ LYGGRAAGRR PRHPRFGSGM
SPLCLHQPFL HAEGGTAGSW CLWPRVPAPP CPSLPLFAPP APSL*

speed

0.25 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