MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000343849
Querying Taster for transcript #2: ENST00000397368
MT speed 0 s - this script 3.786446 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CAV3	disease_causing_automatic	0.999999631158986	simple_aae		affected	0	S141R	single base exchange	rs104893713		show file
CAV3	disease_causing_automatic	0.999999631158986	simple_aae		affected	0	S141R	single base exchange	rs104893713		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999631158986 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM065053)
known disease mutation: rs8291 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:8787520C>GN/A show variant in all transcripts IGV

HGNC symbol

CAV3

Ensembl transcript ID

ENST00000343849

Genbank transcript ID

NM_033337

UniProt peptide

P56539

alteration type

single base exchange

alteration region

CDS

DNA changes

c.423C>G
cDNA.500C>G
g.12035C>G

AA changes

S141R Score: 110 explain score(s)

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

141

frameshift

known variant

Reference ID: rs104893713
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8291 (pathogenic for Long QT syndrome 9|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM065053)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065053)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065053)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.098	1
	2.489	1
(flanking)	1.799	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
Acc marginally increased	12026	wt: 0.4120 / mu: 0.4293 (marginal change - not scored)	wt: CTCTTCGCGGCCCTGGGCCAGGTCTGCAGCAGCATCAAGGT mu: CTCTTCGCGGCCCTGGGCCAGGTCTGCAGGAGCATCAAGGT	ccag\|GTCT
Donor gained	12031	0.50	mu: GGTCTGCAGGAGCAT	TCTG\|cagg

distance from splice site

309

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

141

mutated

not conserved

141

Ptroglodytes

all identical

ENSPTRG00000014581

141

Mmulatta

all identical

ENSMMUG00000009700

141

Fcatus

all identical

ENSFCAG00000014725

182

Mmusculus

all identical

ENSMUSG00000062694

141

Ggallus

all identical

ENSGALG00000008351

145

Trubripes

not conserved

ENSTRUG00000002941

143

Drerio

all identical

ENSDARG00000024141

140

Dmelanogaster

no homologue

Celegans

all identical

T13F2.8

217

Xtropicalis

all identical

ENSXETG00000001440

145

protein features

start (aa)	end (aa)	feature	details
105	151	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

456 / 456

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

152 / 152

position of stopcodon in wt / mu cDNA

533 / 533

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

78 / 78

chromosome

strand

last intron/exon boundary

192

theoretical NMD boundary in CDS

length of CDS

456

coding sequence (CDS) position

423

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

500

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

12035

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

8787520

original gDNA sequence snippet

GCCCTGGGCCAGGTCTGCAGCAGCATCAAGGTGGTGCTGCG

altered gDNA sequence snippet

GCCCTGGGCCAGGTCTGCAGGAGCATCAAGGTGGTGCTGCG

original cDNA sequence snippet

GCCCTGGGCCAGGTCTGCAGCAGCATCAAGGTGGTGCTGCG

altered cDNA sequence snippet

GCCCTGGGCCAGGTCTGCAGGAGCATCAAGGTGGTGCTGCG

wildtype AA sequence

MMAEEHTDLE AQIVKDIHCK EIDLVNRDPK NINEDIVKVD FEDVIAEPVG TYSFDGVWKV
SYTTFTVSKY WCYRLLSTLL GVPLALLWGF LFACISFCHI WAVVPCIKSY LIEIQCISHI
YSLCIRTFCN PLFAALGQVC SSIKVVLRKE V*

mutated AA sequence

MMAEEHTDLE AQIVKDIHCK EIDLVNRDPK NINEDIVKVD FEDVIAEPVG TYSFDGVWKV
SYTTFTVSKY WCYRLLSTLL GVPLALLWGF LFACISFCHI WAVVPCIKSY LIEIQCISHI
YSLCIRTFCN PLFAALGQVC RSIKVVLRKE V*

speed

1.03 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

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999631158986 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM065053)
known disease mutation: rs8291 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:8787520C>GN/A show variant in all transcripts IGV

HGNC symbol

CAV3

Ensembl transcript ID

ENST00000397368

Genbank transcript ID

NM_001234

UniProt peptide

P56539

alteration type

single base exchange

alteration region

CDS

DNA changes

c.423C>G
cDNA.434C>G
g.12035C>G

AA changes

S141R Score: 110 explain score(s)

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

141

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.098	1
	2.489	1
(flanking)	1.799	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
Acc marginally increased	12026	wt: 0.4120 / mu: 0.4293 (marginal change - not scored)	wt: CTCTTCGCGGCCCTGGGCCAGGTCTGCAGCAGCATCAAGGT mu: CTCTTCGCGGCCCTGGGCCAGGTCTGCAGGAGCATCAAGGT	ccag\|GTCT
Donor gained	12031	0.50	mu: GGTCTGCAGGAGCAT	TCTG\|cagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

141

mutated

not conserved

141

Ptroglodytes

all identical

ENSPTRG00000014581

141

Mmulatta

all identical

ENSMMUG00000009700

141

Fcatus

all identical

ENSFCAG00000014725

182

Mmusculus

all identical

ENSMUSG00000062694

141

Ggallus

all identical

ENSGALG00000008351

145

Trubripes

not conserved

ENSTRUG00000002941

143

Drerio

all identical

ENSDARG00000024141

140

Dmelanogaster

no homologue

Celegans

all identical

T13F2.8

217

Xtropicalis

all identical

ENSXETG00000001440

145

protein features

start (aa)	end (aa)	feature	details
105	151	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

456 / 456

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

152 / 152

position of stopcodon in wt / mu cDNA

467 / 467

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

12 / 12

chromosome

strand

last intron/exon boundary

474

theoretical NMD boundary in CDS

412

length of CDS

456

coding sequence (CDS) position

423

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

434

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

12035

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

8787520

original gDNA sequence snippet

GCCCTGGGCCAGGTCTGCAGCAGCATCAAGGTGGTGCTGCG

altered gDNA sequence snippet

GCCCTGGGCCAGGTCTGCAGGAGCATCAAGGTGGTGCTGCG

original cDNA sequence snippet

GCCCTGGGCCAGGTCTGCAGCAGCATCAAGGTGGTGCTGCG

altered cDNA sequence snippet

GCCCTGGGCCAGGTCTGCAGGAGCATCAAGGTGGTGCTGCG

wildtype AA sequence

MMAEEHTDLE AQIVKDIHCK EIDLVNRDPK NINEDIVKVD FEDVIAEPVG TYSFDGVWKV
SYTTFTVSKY WCYRLLSTLL GVPLALLWGF LFACISFCHI WAVVPCIKSY LIEIQCISHI
YSLCIRTFCN PLFAALGQVC SSIKVVLRKE V*

mutated AA sequence

MMAEEHTDLE AQIVKDIHCK EIDLVNRDPK NINEDIVKVD FEDVIAEPVG TYSFDGVWKV
SYTTFTVSKY WCYRLLSTLL GVPLALLWGF LFACISFCHI WAVVPCIKSY LIEIQCISHI
YSLCIRTFCN PLFAALGQVC RSIKVVLRKE V*

speed

0.82 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems