MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000227667
Querying Taster for transcript #2: ENST00000375345
MT speed 0 s - this script 3.471572 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
APOC3	disease_causing_automatic	5.96239858512938e-11	simple_aae		affected	0	T112A	single base exchange	rs121918381		show file
APOC3	disease_causing_automatic	6.33215143475481e-10	simple_aae		affected	0	T94A	single base exchange	rs121918381		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 5.96239858512938e-11 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM870005)
known disease mutation: rs17902 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:116703580A>GN/A show variant in all transcripts IGV

HGNC symbol

APOC3

Ensembl transcript ID

ENST00000375345

Genbank transcript ID

N/A

UniProt peptide

P02656

alteration type

single base exchange

alteration region

CDS

DNA changes

c.334A>G
cDNA.396A>G
g.3159A>G

AA changes

T112A Score: 58 explain score(s)

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

112

frameshift

known variant

Reference ID: rs121918381

database	homozygous (G/G)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	4	4

known disease mutation: rs17902 (pathogenic for Apolipoprotein c-iii, nonglycosylated) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM870005)

known disease mutation at this position, please check HGMD for details (HGMD ID CM870005)
known disease mutation at this position, please check HGMD for details (HGMD ID CM870005)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.802	0
	-0.086	0
(flanking)	0.078	0

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	3153	0.85	mu: AGGTCAGACCAGCTT	GTCA\|gacc

distance from splice site

101

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

112

mutated

not conserved

112

Ptroglodytes

all identical

ENSPTRG00000004315

112

Mmulatta

all identical

ENSMMUG00000016126

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000032081

132

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

354 / 354

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

118 / 118

position of stopcodon in wt / mu cDNA

416 / 416

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

63 / 63

chromosome

strand

last intron/exon boundary

296

theoretical NMD boundary in CDS

183

length of CDS

354

coding sequence (CDS) position

334

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

396

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

3159

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

116703580

original gDNA sequence snippet

TGGACCCTGAGGTCAGACCAACTTCAGCCGTGGCTGCCTGA

altered gDNA sequence snippet

TGGACCCTGAGGTCAGACCAGCTTCAGCCGTGGCTGCCTGA

original cDNA sequence snippet

TGGACCCTGAGGTCAGACCAACTTCAGCCGTGGCTGCCTGA

altered cDNA sequence snippet

TGGACCCTGAGGTCAGACCAGCTTCAGCCGTGGCTGCCTGA

wildtype AA sequence

MGTWGAPHRT LPCRNRGAMQ PRVLLVVALL ALLASARASE AEDASLLSFM QGYMKHATKT
AKDALSSVQE SQVAQQARGW VTDGFSSLKD YWSTVKDKFS EFWDLDPEVR PTSAVAA*

mutated AA sequence

MGTWGAPHRT LPCRNRGAMQ PRVLLVVALL ALLASARASE AEDASLLSFM QGYMKHATKT
AKDALSSVQE SQVAQQARGW VTDGFSSLKD YWSTVKDKFS EFWDLDPEVR PASAVAA*

speed

0.76 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: 6.33215143475481e-10 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM870005)
known disease mutation: rs17902 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:116703580A>GN/A show variant in all transcripts IGV

HGNC symbol

APOC3

Ensembl transcript ID

ENST00000227667

Genbank transcript ID

NM_000040

UniProt peptide

P02656

alteration type

single base exchange

alteration region

CDS

DNA changes

c.280A>G
cDNA.342A>G
g.3159A>G

AA changes

T94A Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs121918381

database	homozygous (G/G)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	4	4

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.802	0
	-0.086	0
(flanking)	0.078	0

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	3153	0.85	mu: AGGTCAGACCAGCTT	GTCA\|gacc

distance from splice site

101

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000004315

112

Mmulatta

all identical

ENSMMUG00000016126

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000032081

132

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
68	99	REGION	Lipid-binding.	lost
93	98	HELIX		lost
94	94	CARBOHYD	O-linked (GalNAc...). /FTId=CAR_000168.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

300 / 300

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

100 / 100

position of stopcodon in wt / mu cDNA

362 / 362

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

63 / 63

chromosome

strand

last intron/exon boundary

242

theoretical NMD boundary in CDS

129

length of CDS

300

coding sequence (CDS) position

280

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

342

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

3159

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

116703580

original gDNA sequence snippet

TGGACCCTGAGGTCAGACCAACTTCAGCCGTGGCTGCCTGA

altered gDNA sequence snippet

TGGACCCTGAGGTCAGACCAGCTTCAGCCGTGGCTGCCTGA

original cDNA sequence snippet

TGGACCCTGAGGTCAGACCAACTTCAGCCGTGGCTGCCTGA

altered cDNA sequence snippet

TGGACCCTGAGGTCAGACCAGCTTCAGCCGTGGCTGCCTGA

wildtype AA sequence

MQPRVLLVVA LLALLASARA SEAEDASLLS FMQGYMKHAT KTAKDALSSV QESQVAQQAR
GWVTDGFSSL KDYWSTVKDK FSEFWDLDPE VRPTSAVAA*

mutated AA sequence

MQPRVLLVVA LLALLASARA SEAEDASLLS FMQGYMKHAT KTAKDALSSV QESQVAQQAR
GWVTDGFSSL KDYWSTVKDK FSEFWDLDPE VRPASAVAA*

speed

0.76 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems