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: ENST00000585973
Querying Taster for transcript #2: ENST00000321600
MT speed 0 s - this script 3.371734 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DYNAP	polymorphism_automatic	3.79196674060722e-12	simple_aae				T189P	single base exchange	rs9947055		show file
DYNAP	polymorphism_automatic	1.52059476121735e-11	simple_aae				T137P	single base exchange	rs9947055		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999996208 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:52265308A>CN/A show variant in all transcripts IGV

HGNC symbol

DYNAP

Ensembl transcript ID

ENST00000321600

Genbank transcript ID

NM_173629

UniProt peptide

Q8N1N2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.565A>C
cDNA.611A>C
g.10321A>C

AA changes

T189P Score: 38 explain score(s)

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

189

frameshift

known variant

Reference ID: rs9947055

database	homozygous (C/C)	heterozygous	allele carriers
1000G	752	1184	1936
ExAC	17567	-2367	15200

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.045	0
	-0.217	0
(flanking)	0.847	0.001

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

265

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

189

mutated

not conserved

189

Ptroglodytes

all identical

ENSPTRG00000010037

189

Mmulatta

all identical

ENSMMUG00000013356

187

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000024512

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
172	207	COMPBIAS	Thr-rich.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

633 / 633

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

211 / 211

position of stopcodon in wt / mu cDNA

679 / 679

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

47 / 47

chromosome

strand

last intron/exon boundary

347

theoretical NMD boundary in CDS

250

length of CDS

633

coding sequence (CDS) position

565

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

611

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

10321

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

52265308

original gDNA sequence snippet

GTACAGCCACTGAATCTACAACTTCAACAGCTACAGCTGCC

altered gDNA sequence snippet

GTACAGCCACTGAATCTACACCTTCAACAGCTACAGCTGCC

original cDNA sequence snippet

GTACAGCCACTGAATCTACAACTTCAACAGCTACAGCTGCC

altered cDNA sequence snippet

GTACAGCCACTGAATCTACACCTTCAACAGCTACAGCTGCC

wildtype AA sequence

MVADIKGNEQ IEKYSWREAC DTGSSRMDRK HGKYILNVEH SENQPPITHP NDQEAHSSIC
WCLPSNDITS DVSPNLTGVC VNPGILAHSR CLQSESCNTQ VKEYCRNDWS MWKVFLACLL
ACVIMTAIGV LIICLVNNKG SANSSIVIQL STNDGECVTV KPGTPSPACP PTMTTTSTVP
ASTATESTTS TATAATTSTE PITVAPTDHL *

mutated AA sequence

speed

0.38 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

polymorphism

Model: simple_aae, prob: 0.999999999984794 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:52265308A>CN/A show variant in all transcripts IGV

HGNC symbol

DYNAP

Ensembl transcript ID

ENST00000585973

Genbank transcript ID

N/A

UniProt peptide

Q8N1N2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.409A>C
cDNA.500A>C
g.10321A>C

AA changes

T137P Score: 38 explain score(s)

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

137

frameshift

known variant

Reference ID: rs9947055

database	homozygous (C/C)	heterozygous	allele carriers
1000G	752	1184	1936
ExAC	17567	-2367	15200

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.045	0
	-0.217	0
(flanking)	0.847	0.001

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

265

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

137

mutated

not conserved

137

Ptroglodytes

all identical

ENSPTRG00000010037

189

Mmulatta

all identical

ENSMMUG00000013356

187

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000024512

140

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

477 / 477

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

159 / 159

position of stopcodon in wt / mu cDNA

568 / 568

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

92 / 92

chromosome

strand

last intron/exon boundary

236

theoretical NMD boundary in CDS

length of CDS

477

coding sequence (CDS) position

409

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

500

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

10321

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

52265308

original gDNA sequence snippet

GTACAGCCACTGAATCTACAACTTCAACAGCTACAGCTGCC

altered gDNA sequence snippet

GTACAGCCACTGAATCTACACCTTCAACAGCTACAGCTGCC

original cDNA sequence snippet

GTACAGCCACTGAATCTACAACTTCAACAGCTACAGCTGCC

altered cDNA sequence snippet

GTACAGCCACTGAATCTACACCTTCAACAGCTACAGCTGCC

wildtype AA sequence

MEYQLLDIKG NEQIEKYSWR EACDTGSSRM DRKHGKYILN VEHSENQPVK EYCRNDWSMW
KVFLACLLAC VIMTAIGVLI ICLVNNKGSA NSSIVIQLST NDGECVTVKP GTPSPACPPT
MTTTSTVPAS TATESTTSTA TAATTSTEPI TVAPTDHL*

mutated AA sequence

MEYQLLDIKG NEQIEKYSWR EACDTGSSRM DRKHGKYILN VEHSENQPVK EYCRNDWSMW
KVFLACLLAC VIMTAIGVLI ICLVNNKGSA NSSIVIQLST NDGECVTVKP GTPSPACPPT
MTTTSTVPAS TATESTPSTA TAATTSTEPI TVAPTDHL*

speed

1.05 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems