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: ENST00000369792
MT speed 0 s - this script 2.206043 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ALX3	disease_causing_automatic	0.999999683242573	simple_aae			0	R183W	single base exchange	rs121908168		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999683242573 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM092883)
known disease mutation: rs4645 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:110607256G>AN/A show variant in all transcripts IGV

HGNC symbol

ALX3

Ensembl transcript ID

ENST00000369792

Genbank transcript ID

NM_006492

UniProt peptide

O95076

alteration type

single base exchange

alteration region

CDS

DNA changes

c.547C>T
cDNA.547C>T
g.5979C>T

AA changes

R183W Score: 101 explain score(s)

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

183

frameshift

known variant

Reference ID: rs121908168

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs4645 (pathogenic for Frontonasal dysplasia 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM092883)

known disease mutation at this position, please check HGMD for details (HGMD ID CM092883)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092883)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.041	1
	0.375	0.999
(flanking)	1.579	1

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	5975	wt: 0.3243 / mu: 0.3424 (marginal change - not scored)	wt: ACCCACTATCCTGATGTGTATGCCCGGGAGCAGCTGGCCCT mu: ACCCACTATCCTGATGTGTATGCCTGGGAGCAGCTGGCCCT	gtat\|GCCC
Acc marginally increased	5979	wt: 0.4901 / mu: 0.5200 (marginal change - not scored)	wt: ACTATCCTGATGTGTATGCCCGGGAGCAGCTGGCCCTGCGC mu: ACTATCCTGATGTGTATGCCTGGGAGCAGCTGGCCCTGCGC	gccc\|GGGA
Acc marginally increased	5980	wt: 0.2344 / mu: 0.2436 (marginal change - not scored)	wt: CTATCCTGATGTGTATGCCCGGGAGCAGCTGGCCCTGCGCA mu: CTATCCTGATGTGTATGCCTGGGAGCAGCTGGCCCTGCGCA	cccg\|GGAG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

183

mutated

not conserved

183

Ptroglodytes

all identical

ENSPTRG00000001070

183

Mmulatta

all identical

ENSMMUG00000031857

183

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000014603

183

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000003032

Drerio

all identical

ENSDARG00000091086

200

Dmelanogaster

all identical

FBgn0053980

260

Celegans

all identical

W03A3.1

166

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
153	212	DNA_BIND	Homeobox.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1032 / 1032

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

344 / 344

position of stopcodon in wt / mu cDNA

1032 / 1032

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

724

theoretical NMD boundary in CDS

673

length of CDS

1032

coding sequence (CDS) position

547

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

547

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

5979

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

110607256

original gDNA sequence snippet

ACTATCCTGATGTGTATGCCCGGGAGCAGCTGGCCCTGCGC

altered gDNA sequence snippet

ACTATCCTGATGTGTATGCCTGGGAGCAGCTGGCCCTGCGC

original cDNA sequence snippet

ACTATCCTGATGTGTATGCCCGGGAGCAGCTGGCCCTGCGC

altered cDNA sequence snippet

ACTATCCTGATGTGTATGCCTGGGAGCAGCTGGCCCTGCGC

wildtype AA sequence

MDPEHCAPFR VGPAPGPYVA SGDEPPGPQG TPAAAPHLHP APPRGPRLTR FPACGPLEPY
LPEPAKPPAK YLQDLGPGPA LNGGHFYEGP AEAEEKTSKA ASFPQLPLDC RGGPRDGPSN
LQGSPGPCLA SLHLPLSPGL PDSMELAKNK SKKRRNRTTF STFQLEELEK VFQKTHYPDV
YAREQLALRT DLTEARVQVW FQNRRAKWRK RERYGKIQEG RNPFTAAYDI SVLPRTDSHP
QLQNSLWASP GSGSPGGPCL VSPEGIPSPC MSPYSHPHGS VAGFMGVPAP SAAHPGIYSI
HGFPPTLGGH SFEPSSDGDY KSPSLVSLRV KPKEPPGLLN WTT*

mutated AA sequence

MDPEHCAPFR VGPAPGPYVA SGDEPPGPQG TPAAAPHLHP APPRGPRLTR FPACGPLEPY
LPEPAKPPAK YLQDLGPGPA LNGGHFYEGP AEAEEKTSKA ASFPQLPLDC RGGPRDGPSN
LQGSPGPCLA SLHLPLSPGL PDSMELAKNK SKKRRNRTTF STFQLEELEK VFQKTHYPDV
YAWEQLALRT DLTEARVQVW FQNRRAKWRK RERYGKIQEG RNPFTAAYDI SVLPRTDSHP
QLQNSLWASP GSGSPGGPCL VSPEGIPSPC MSPYSHPHGS VAGFMGVPAP SAAHPGIYSI
HGFPPTLGGH SFEPSSDGDY KSPSLVSLRV KPKEPPGLLN WTT*

speed

0.19 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems