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 3.375669 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ALX4	disease_causing_automatic	0.99999999951617	simple_aae		affected	0	R272P	single base exchange	rs104894196		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999951617 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002931)
known disease mutation: rs5017 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:44289135C>GN/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.815G>C
cDNA.919G>C
g.42582G>C

AA changes

R272P Score: 103 explain score(s)

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

272

frameshift

known variant

Reference ID: rs104894196
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs5017 (pathogenic for Parietal foramina 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002931)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002931)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002931)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.217	1
	5.907	1
(flanking)	0.908	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
Donor increased	42582	wt: 0.74 / mu: 0.93	wt: GAAGCGGGAGCGTTT mu: GAAGCCGGAGCGTTT	AGCG\|ggag
Donor increased	42580	wt: 0.46 / mu: 0.74	wt: AGGAAGCGGGAGCGT mu: AGGAAGCCGGAGCGT	GAAG\|cggg
Donor marginally increased	42575	wt: 0.4868 / mu: 0.5352 (marginal change - not scored)	wt: AGTGGAGGAAGCGGG mu: AGTGGAGGAAGCCGG	TGGA\|ggaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

272

mutated

not conserved

272

Ptroglodytes

all identical

ENSPTRG00000003529

227

Mmulatta

all identical

ENSMMUG00000013097

270

Fcatus

all identical

ENSFCAG00000005620

269

Mmusculus

all identical

ENSMUSG00000040310

260

Ggallus

all identical

ENSGALG00000008024

250

Trubripes

all identical

ENSTRUG00000017295

226

Drerio

all identical

ENSDARG00000088332

233

Dmelanogaster

all conserved

FBgn0020617

586

Celegans

all conserved

ZK265.4

118

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
214	273	DNA_BIND	Homeobox.	lost
391	404	MOTIF	OAR.	might get lost (downstream of altered splice site)

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

815

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

919

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

42582

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

44289135

original gDNA sequence snippet

AAGGGCCAAGTGGAGGAAGCGGGAGCGTTTTGGGCAGATGC

altered gDNA sequence snippet

AAGGGCCAAGTGGAGGAAGCCGGAGCGTTTTGGGCAGATGC

original cDNA sequence snippet

AAGGGCCAAGTGGAGGAAGCGGGAGCGTTTTGGGCAGATGC

altered cDNA sequence snippet

AAGGGCCAAGTGGAGGAAGCCGGAGCGTTTTGGGCAGATGC

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 KGKKRRNRTT FTSYQLEELE KVFQKTHYPD
VYAREQLAMR TDLTEARVQV WFQNRRAKWR KPERFGQMQQ VRTHFSTAYE LPLLTRAENY
AQIQNPSWLG NNGAASPVPA CVVPCDPVPA CMSPHAHPPG SGASSVTDFL SVSGAGSHVG
QTHMGSLFGA ASLSPGLNGY ELNGEPDRKT SSIAALRMKA KEHSAAISWA T*

speed

1.27 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