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: ENST00000319144
MT speed 0 s - this script 2.985795 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ALOX12B	disease_causing_automatic	0.999897524221862	simple_aae		affected	0	H578Q	single base exchange	rs137853024		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999897524221862 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM020009)
known disease mutation: rs6084 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:7976996G>TN/A show variant in all transcripts IGV

HGNC symbol

ALOX12B

Ensembl transcript ID

ENST00000319144

Genbank transcript ID

NM_001139

UniProt peptide

O75342

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1734C>A
cDNA.1995C>A
g.14026C>A

AA changes

H578Q Score: 24 explain score(s)

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

578

frameshift

known variant

Reference ID: rs137853024

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs6084 (pathogenic for Autosomal recessive congenital ichthyosis 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM020009)

known disease mutation at this position, please check HGMD for details (HGMD ID CM020009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM020009)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.766	1
	0.041	0.994
(flanking)	4.36	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	14021	wt: 0.56 / mu: 0.96	wt: CTGCCAAGCACGCTG mu: CTGCCAAGCAAGCTG	GCCA\|agca
Donor gained	14026	0.31	mu: AAGCAAGCTGCTGTC	GCAA\|gctg
Donor gained	14022	0.85	mu: TGCCAAGCAAGCTGC	CCAA\|gcaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

578

mutated

not conserved

578

Ptroglodytes

all identical

ENSPTRG00000008723

578

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000032807

578

Ggallus

all identical

ENSGALG00000013280

558

Trubripes

no homologue

Drerio

all identical

ENSDARG00000016789

540

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000018683

562

protein features

start (aa)	end (aa)	feature	details
120	701	DOMAIN	Lipoxygenase.	lost
578	578	METAL	Iron; catalytic (By similarity).	lost
582	582	METAL	Iron; catalytic (By similarity).	might get lost (downstream of altered splice site)
701	701	METAL	Iron; via carboxylate; catalytic (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2106 / 2106

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

702 / 702

position of stopcodon in wt / mu cDNA

2367 / 2367

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

262 / 262

chromosome

strand

-1

last intron/exon boundary

2188

theoretical NMD boundary in CDS

1876

length of CDS

2106

coding sequence (CDS) position

1734

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

1995

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

14026

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

7976996

original gDNA sequence snippet

TACACCTGCTCTGCCAAGCACGCTGCTGTCAACACAGGCCA

altered gDNA sequence snippet

TACACCTGCTCTGCCAAGCAAGCTGCTGTCAACACAGGCCA

original cDNA sequence snippet

TACACCTGCTCTGCCAAGCACGCTGCTGTCAACACAGGCCA

altered cDNA sequence snippet

TACACCTGCTCTGCCAAGCAAGCTGCTGTCAACACAGGCCA

wildtype AA sequence

MATYKVRVAT GTDLLSGTRD SISLTIVGTQ GESHKQLLNH FGRDFATGAV GQYTVQCPQD
LGELIIIRLH KERYAFFPKD PWYCNYVQIC APNGRIYHFP AYQWMDGYET LALREATGKT
TADDSLPVLL EHRKEEIRAK QDFYHWRVFL PGLPSYVHIP SYRPPVRRHR NPNRPEWNGY
IPGFPILINF KATKFLNLNL RYSFLKTASF FVRLGPMALA FKVRGLLDCK HSWKRLKDIR
KIFPGKKSVV SEYVAEHWAE DTFFGYQYLN GVNPGLIRRC TRIPDKFPVT DDMVAPFLGE
GTCLQAELEK GNIYLADYRI MEGIPTVELS GRKQHHCAPL CLLHFGPEGK MMPIAIQLSQ
TPGPDCPIFL PSDSEWDWLL AKTWVRYAEF YSHEAIAHLL ETHLIAEAFC LALLRNLPMC
HPLYKLLIPH TRYTVQINSI GRAVLLNEGG LSAKGMSLGV EGFAGVMVRA LSELTYDSLY
LPNDFVERGV QDLPGYYYRD DSLAVWNALE KYVTEIITYY YPSDAAVEGD PELQSWVQEI
FKECLLGRES SGFPRCLRTV PELIRYVTIV IYTCSAKHAA VNTGQMEFTA WMPNFPASMR
NPPIQTKGLT TLETFMDTLP DVKTTCITLL VLWTLSREPD DRRPLGHFPD IHFVEEAPRR
SIEAFRQRLN QISHDIRQRN KCLPIPYYYL DPVLIENSIS I*

mutated AA sequence

MATYKVRVAT GTDLLSGTRD SISLTIVGTQ GESHKQLLNH FGRDFATGAV GQYTVQCPQD
LGELIIIRLH KERYAFFPKD PWYCNYVQIC APNGRIYHFP AYQWMDGYET LALREATGKT
TADDSLPVLL EHRKEEIRAK QDFYHWRVFL PGLPSYVHIP SYRPPVRRHR NPNRPEWNGY
IPGFPILINF KATKFLNLNL RYSFLKTASF FVRLGPMALA FKVRGLLDCK HSWKRLKDIR
KIFPGKKSVV SEYVAEHWAE DTFFGYQYLN GVNPGLIRRC TRIPDKFPVT DDMVAPFLGE
GTCLQAELEK GNIYLADYRI MEGIPTVELS GRKQHHCAPL CLLHFGPEGK MMPIAIQLSQ
TPGPDCPIFL PSDSEWDWLL AKTWVRYAEF YSHEAIAHLL ETHLIAEAFC LALLRNLPMC
HPLYKLLIPH TRYTVQINSI GRAVLLNEGG LSAKGMSLGV EGFAGVMVRA LSELTYDSLY
LPNDFVERGV QDLPGYYYRD DSLAVWNALE KYVTEIITYY YPSDAAVEGD PELQSWVQEI
FKECLLGRES SGFPRCLRTV PELIRYVTIV IYTCSAKQAA VNTGQMEFTA WMPNFPASMR
NPPIQTKGLT TLETFMDTLP DVKTTCITLL VLWTLSREPD DRRPLGHFPD IHFVEEAPRR
SIEAFRQRLN QISHDIRQRN KCLPIPYYYL DPVLIENSIS I*

speed

0.93 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