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: ENST00000269143
MT speed 0 s - this script 3.016689 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AFG3L2	disease_causing_automatic	0.999999999758457	simple_aae		affected	0	E691K	single base exchange	rs151344520		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999758457 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM088028)
known disease mutation: rs5470 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:12337444C>TN/A show variant in all transcripts IGV

HGNC symbol

AFG3L2

Ensembl transcript ID

ENST00000269143

Genbank transcript ID

NM_006796

UniProt peptide

Q9Y4W6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2071G>A
cDNA.2303G>A
g.39870G>A

AA changes

E691K Score: 56 explain score(s)

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

691

frameshift

known variant

Reference ID: rs151344520
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs5470 (pathogenic for Spinocerebellar ataxia type 28) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM088028)

known disease mutation at this position, please check HGMD for details (HGMD ID CM088028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM088028)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.741	1
	5.725	1
(flanking)	-0.011	0.99

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 marginally increased	39872	wt: 0.8674 / mu: 0.9343 (marginal change - not scored)	wt: AGTGAAGCCACTGCA mu: AGTAAAGCCACTGCA	TGAA\|gcca
Donor increased	39862	wt: 0.47 / mu: 0.60	wt: GAAACCTTACAGTGA mu: GAAACCTTACAGTAA	AACC\|ttac

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

691

mutated

all conserved

691

Ptroglodytes

all identical

ENSPTRG00000009879

706

Mmulatta

all identical

ENSMMUG00000021125

709

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000024527

690

Ggallus

all identical

ENSGALG00000013853

691

Trubripes

no homologue

Drerio

all identical

ENSDARG00000062272

686

Dmelanogaster

all identical

FBgn0036702

709

Celegans

all identical

Y47G6A.10

676

Xtropicalis

all identical

ENSXETG00000032431

697

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2394 / 2394

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

798 / 798

position of stopcodon in wt / mu cDNA

2626 / 2626

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

233 / 233

chromosome

strand

-1

last intron/exon boundary

2408

theoretical NMD boundary in CDS

2125

length of CDS

2394

coding sequence (CDS) position

2071

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

2303

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

39870

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

12337444

original gDNA sequence snippet

TATTGGAGAAACCTTACAGTGAAGCCACTGCAAGATTGATA

altered gDNA sequence snippet

TATTGGAGAAACCTTACAGTAAAGCCACTGCAAGATTGATA

original cDNA sequence snippet

TATTGGAGAAACCTTACAGTGAAGCCACTGCAAGATTGATA

altered cDNA sequence snippet

TATTGGAGAAACCTTACAGTAAAGCCACTGCAAGATTGATA

wildtype AA sequence

MAHRCLRLWG RGGCWPRGLQ QLLVPGGVGP GEQPCLRTLY RFVTTQARAS RNSLLTDIIA
AYQRFCSRPP KGFEKYFPNG KNGKKASEPK EVMGEKKESK PAATTRSSGG GGGGGGKRGG
KKDDSHWWSR FQKGDIPWDD KDFRMFFLWT ALFWGGVMFY LLLKRSGREI TWKDFVNNYL
SKGVVDRLEV VNKRFVRVTF TPGKTPVDGQ YVWFNIGSVD TFERNLETLQ QELGIEGENR
VPVVYIAESD GSFLLSMLPT VLIIAFLLYT IRRGPAGIGR TGRGMGGLFS VGETTAKVLK
DEIDVKFKDV AGCEEAKLEI MEFVNFLKNP KQYQDLGAKI PKGAILTGPP GTGKTLLAKA
TAGEANVPFI TVSGSEFLEM FVGVGPARVR DLFALARKNA PCILFIDEID AVGRKRGRGN
FGGQSEQENT LNQLLVEMDG FNTTTNVVIL AGTNRPDILD PALLRPGRFD RQIFIGPPDI
KGRASIFKVH LRPLKLDSTL EKDKLARKLA SLTPGFSGAD VANVCNEAAL IAARHLSDSI
NQKHFEQAIE RVIGGLEKKT QVLQPEEKKT VAYHEAGHAV AGWYLEHADP LLKVSIIPRG
KGLGYAQYLP KEQYLYTKEQ LLDRMCMTLG GRVSEEIFFG RITTGAQDDL RKVTQSAYAQ
IVQFGMNEKV GQISFDLPRQ GDMVLEKPYS EATARLIDDE VRILINDAYK RTVALLTEKK
ADVEKVALLL LEKEVLDKND MVELLGPRPF AEKSTYEEFV EGTGSLDEDT SLPEGLKDWN
KEREKEKEEP PGEKVAN*

mutated AA sequence

MAHRCLRLWG RGGCWPRGLQ QLLVPGGVGP GEQPCLRTLY RFVTTQARAS RNSLLTDIIA
AYQRFCSRPP KGFEKYFPNG KNGKKASEPK EVMGEKKESK PAATTRSSGG GGGGGGKRGG
KKDDSHWWSR FQKGDIPWDD KDFRMFFLWT ALFWGGVMFY LLLKRSGREI TWKDFVNNYL
SKGVVDRLEV VNKRFVRVTF TPGKTPVDGQ YVWFNIGSVD TFERNLETLQ QELGIEGENR
VPVVYIAESD GSFLLSMLPT VLIIAFLLYT IRRGPAGIGR TGRGMGGLFS VGETTAKVLK
DEIDVKFKDV AGCEEAKLEI MEFVNFLKNP KQYQDLGAKI PKGAILTGPP GTGKTLLAKA
TAGEANVPFI TVSGSEFLEM FVGVGPARVR DLFALARKNA PCILFIDEID AVGRKRGRGN
FGGQSEQENT LNQLLVEMDG FNTTTNVVIL AGTNRPDILD PALLRPGRFD RQIFIGPPDI
KGRASIFKVH LRPLKLDSTL EKDKLARKLA SLTPGFSGAD VANVCNEAAL IAARHLSDSI
NQKHFEQAIE RVIGGLEKKT QVLQPEEKKT VAYHEAGHAV AGWYLEHADP LLKVSIIPRG
KGLGYAQYLP KEQYLYTKEQ LLDRMCMTLG GRVSEEIFFG RITTGAQDDL RKVTQSAYAQ
IVQFGMNEKV GQISFDLPRQ GDMVLEKPYS KATARLIDDE VRILINDAYK RTVALLTEKK
ADVEKVALLL LEKEVLDKND MVELLGPRPF AEKSTYEEFV EGTGSLDEDT SLPEGLKDWN
KEREKEKEEP PGEKVAN*

speed

1.01 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