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: ENST00000393262
MT speed 0 s - this script 2.929407 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BBS10	disease_causing_automatic	0.992029312649072	simple_aae		affected	0	S311A	single base exchange	rs137852837		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.992029312649072 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM063863)
known disease mutation: rs1331 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:76740834A>CN/A show variant in all transcripts IGV

HGNC symbol

BBS10

Ensembl transcript ID

ENST00000393262

Genbank transcript ID

NM_024685

UniProt peptide

Q8TAM1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.931T>G
cDNA.1015T>G
g.1389T>G

AA changes

S311A Score: 99 explain score(s)

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

311

frameshift

known variant

Reference ID: rs137852837
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs1331 (pathogenic for Bardet-Biedl syndrome 10|Bardet-Biedl syndrome|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM063863)

known disease mutation at this position, please check HGMD for details (HGMD ID CM063863)
known disease mutation at this position, please check HGMD for details (HGMD ID CM063863)

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.374	0.999
	2.171	0.987
(flanking)	-0.866	0.687

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 gained	1388	0.32	mu: CTCATAGCTAGTGTG	CATA\|gcta

distance from splice site

734

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

311

mutated

all conserved

311

Ptroglodytes

all identical

ENSPTRG00000005241

311

Mmulatta

all identical

ENSMMUG00000017862

311

Fcatus

all identical

ENSFCAG00000014007

284

Mmusculus

all conserved

ENSMUSG00000035759

308

Ggallus

all identical

ENSGALG00000010241

Trubripes

no homologue

Drerio

all identical

ENSDARG00000069515

293

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000031389

307

protein features

start (aa)	end (aa)	feature	details
514	514	CONFLICT	T -> S (in Ref. 2; BAB15695).	might get lost (downstream of altered splice site)
586	586	CONFLICT	S -> Y (in Ref. 2; BAB15695).	might get lost (downstream of altered splice site)
607	607	CONFLICT	E -> D (in Ref. 1; AAH26355).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2172 / 2172

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

724 / 724

position of stopcodon in wt / mu cDNA

2256 / 2256

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

85 / 85

chromosome

strand

-1

last intron/exon boundary

282

theoretical NMD boundary in CDS

147

length of CDS

2172

coding sequence (CDS) position

931

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

1015

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

1389

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

76740834

original gDNA sequence snippet

AGAATGTAAAATTGCTCATATCTAGTGTGAAACAACCAGAT

altered gDNA sequence snippet

AGAATGTAAAATTGCTCATAGCTAGTGTGAAACAACCAGAT

original cDNA sequence snippet

AGAATGTAAAATTGCTCATATCTAGTGTGAAACAACCAGAT

altered cDNA sequence snippet

AGAATGTAAAATTGCTCATAGCTAGTGTGAAACAACCAGAT

wildtype AA sequence

MLSSMAAAGS VKAALQVAEV LEAIVSCCVG PEGRQVLCTK PTGEVLLSRN GGRLLEALHL
EHPIARMIVD CVSSHLKKTG DGAKTFIIFL CHLLRGLHAI TDREKDPLMC ENIQTHGRHW
KNCSRWKFIS QALLTFQTQI LDGIMDQYLS RHFLSIFSSA KERTLCRSSL ELLLEAYFCG
RVGRNNHKFI SQLMCDYFFK CMTCKSGIGV FELVDDHFVE LNVGVTGLPV SDSRIIAGLV
LQKDFSVYRP ADGDMRMVIV TETIQPLFST SGSEFILNSE AQFQTSQFWI MEKTKAIMKH
LHSQNVKLLI SSVKQPDLVS YYAGVNGISV VECLSSEEVS LIRRIIGLSP FVPPQAFSQC
EIPNTALVKF CKPLILRSKR YVHLGLISTC AFIPHSIVLC GPVHGLIEQH EDALHGALKM
LRQLFKDLDL NYMTQTNDQN GTSSLFIYKN SGESYQAPDP GNGSIQRPYQ DTVAENKDAL
EKTQTYLKVH SNLVIPDVEL ETYIPYSTPT LTPTDTFQTV ETLTCLSLER NRLTDYYEPL
LKNNSTAYST RGNRIEISYE NLQVTNITRK GSMLPVSCKL PNMGTSQSYL SSSMPAGCVL
PVGGNFEILL HYYLLNYAKK CHQSEETMVS MIIANALLGI PKVLYKSKTG KYSFPHTYIR
AVHALQTNQP LVSSQTGLES VMGKYQLLTS VLQCLTKILT IDMVITVKRH PQKVHNQDSE
DEL*

mutated AA sequence

MLSSMAAAGS VKAALQVAEV LEAIVSCCVG PEGRQVLCTK PTGEVLLSRN GGRLLEALHL
EHPIARMIVD CVSSHLKKTG DGAKTFIIFL CHLLRGLHAI TDREKDPLMC ENIQTHGRHW
KNCSRWKFIS QALLTFQTQI LDGIMDQYLS RHFLSIFSSA KERTLCRSSL ELLLEAYFCG
RVGRNNHKFI SQLMCDYFFK CMTCKSGIGV FELVDDHFVE LNVGVTGLPV SDSRIIAGLV
LQKDFSVYRP ADGDMRMVIV TETIQPLFST SGSEFILNSE AQFQTSQFWI MEKTKAIMKH
LHSQNVKLLI ASVKQPDLVS YYAGVNGISV VECLSSEEVS LIRRIIGLSP FVPPQAFSQC
EIPNTALVKF CKPLILRSKR YVHLGLISTC AFIPHSIVLC GPVHGLIEQH EDALHGALKM
LRQLFKDLDL NYMTQTNDQN GTSSLFIYKN SGESYQAPDP GNGSIQRPYQ DTVAENKDAL
EKTQTYLKVH SNLVIPDVEL ETYIPYSTPT LTPTDTFQTV ETLTCLSLER NRLTDYYEPL
LKNNSTAYST RGNRIEISYE NLQVTNITRK GSMLPVSCKL PNMGTSQSYL SSSMPAGCVL
PVGGNFEILL HYYLLNYAKK CHQSEETMVS MIIANALLGI PKVLYKSKTG KYSFPHTYIR
AVHALQTNQP LVSSQTGLES VMGKYQLLTS VLQCLTKILT IDMVITVKRH PQKVHNQDSE
DEL*

speed

0.87 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