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: ENST00000329255
MT speed 0 s - this script 2.312518 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ALX4	disease_causing_automatic	0.999999999673026	simple_aae			0	R218Q	single base exchange	rs104894193		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999673026 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010011)
known disease mutation: rs5015 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:44297022C>TN/A show variant in all transcripts IGV

HGNC symbol

ALX4

Ensembl transcript ID

ENST00000329255

Genbank transcript ID

NM_021926

UniProt peptide

Q9H161

alteration type

single base exchange

alteration region

CDS

DNA changes

c.653G>A
cDNA.757G>A
g.34695G>A

AA changes

R218Q Score: 43 explain score(s)

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

218

frameshift

known variant

Reference ID: rs104894193

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

known disease mutation: rs5015 (pathogenic for Parietal foramina 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010011)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010011)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010011)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.098	0.615
	5.205	1
(flanking)	2.49	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

125

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

218

mutated

all conserved

218

Ptroglodytes

all identical

ENSPTRG00000003529

173

Mmulatta

all identical

ENSMMUG00000013097

216

Fcatus

all identical

ENSFCAG00000005620

215

Mmusculus

all identical

ENSMUSG00000040310

206

Ggallus

all identical

ENSGALG00000008024

196

Trubripes

all identical

ENSTRUG00000017295

179

Drerio

all identical

ENSDARG00000088332

180

Dmelanogaster

all identical

FBgn0020617

532

Celegans

all identical

ZK265.4

KIADKK

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
214	273	DNA_BIND	Homeobox.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1236 / 1236

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

412 / 412

position of stopcodon in wt / mu cDNA

1340 / 1340

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

105 / 105

chromosome

strand

-1

last intron/exon boundary

1011

theoretical NMD boundary in CDS

856

length of CDS

1236

coding sequence (CDS) position

653

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

757

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

34695

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

44297022

original gDNA sequence snippet

GGGCAAGAAGCGGCGGAACCGGACCACCTTCACCAGCTACC

altered gDNA sequence snippet

GGGCAAGAAGCGGCGGAACCAGACCACCTTCACCAGCTACC

original cDNA sequence snippet

GGGCAAGAAGCGGCGGAACCGGACCACCTTCACCAGCTACC

altered cDNA sequence snippet

GGGCAAGAAGCGGCGGAACCAGACCACCTTCACCAGCTACC

wildtype AA sequence

MNAETCVSYC ESPAAAMDAY YSPVSQSREG SSPFRAFPGG DKFGTTFLSA AAKAQGFGDA
KSRARYGAGQ QDLATPLESG AGARGSFNKF QPQPSTPQPQ PPPQPQPQQQ QPQPQPPAQP
HLYLQRGACK TPPDGSLKLQ EGSSGHSAAL QVPCYAKESS LGEPELPPDS DTVGMDSSYL
SVKEAGVKGP QDRASSDLPS PLEKADSESN KGKKRRNRTT FTSYQLEELE KVFQKTHYPD
VYAREQLAMR TDLTEARVQV WFQNRRAKWR KRERFGQMQQ VRTHFSTAYE LPLLTRAENY
AQIQNPSWLG NNGAASPVPA CVVPCDPVPA CMSPHAHPPG SGASSVTDFL SVSGAGSHVG
QTHMGSLFGA ASLSPGLNGY ELNGEPDRKT SSIAALRMKA KEHSAAISWA T*

mutated AA sequence

MNAETCVSYC ESPAAAMDAY YSPVSQSREG SSPFRAFPGG DKFGTTFLSA AAKAQGFGDA
KSRARYGAGQ QDLATPLESG AGARGSFNKF QPQPSTPQPQ PPPQPQPQQQ QPQPQPPAQP
HLYLQRGACK TPPDGSLKLQ EGSSGHSAAL QVPCYAKESS LGEPELPPDS DTVGMDSSYL
SVKEAGVKGP QDRASSDLPS PLEKADSESN KGKKRRNQTT FTSYQLEELE KVFQKTHYPD
VYAREQLAMR TDLTEARVQV WFQNRRAKWR KRERFGQMQQ VRTHFSTAYE LPLLTRAENY
AQIQNPSWLG NNGAASPVPA CVVPCDPVPA CMSPHAHPPG SGASSVTDFL SVSGAGSHVG
QTHMGSLFGA ASLSPGLNGY ELNGEPDRKT SSIAALRMKA KEHSAAISWA T*

speed

0.31 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