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: ENST00000317378
Querying Taster for transcript #2: ENST00000426877
MT speed 0 s - this script 2.374356 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TRAPPC5	polymorphism_automatic	8.55680075295684e-06	simple_aae		affected		S52A	single base exchange	rs6952		show file
TRAPPC5	polymorphism_automatic	8.55680075295684e-06	simple_aae		affected		S52A	single base exchange	rs6952		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999991443199247 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:7747293T>GN/A show variant in all transcripts IGV

HGNC symbol

TRAPPC5

Ensembl transcript ID

ENST00000317378

Genbank transcript ID

NM_174894

UniProt peptide

Q8IUR0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.154T>G
cDNA.341T>G
g.1533T>G

AA changes

S52A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs6952

database	homozygous (G/G)	heterozygous	allele carriers
1000G	361	1071	1432
ExAC	2958	13135	16093

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.614	1
	1.344	1
(flanking)	1.474	0.996

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 increased	1525	wt: 0.53 / mu: 0.66	wt: CCGCGTCTTCTCCGTGGCCGAGCTGCAGTCGCGCCTGGCCG mu: CCGCGTCTTCTCCGTGGCCGAGCTGCAGGCGCGCCTGGCCG	ccga\|GCTG

distance from splice site

166

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000010400

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000040236

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000002717

Drerio

all conserved

ENSDARG00000026068

Dmelanogaster

all conserved

FBgn0033962

Celegans

not conserved

Y57A10A.16

Xtropicalis

all conserved

ENSXETG00000001289

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

567 / 567

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

189 / 189

position of stopcodon in wt / mu cDNA

754 / 754

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

188 / 188

chromosome

strand

last intron/exon boundary

176

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

567

coding sequence (CDS) position

154

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

341

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

1533

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

7747293

original gDNA sequence snippet

TCTCCGTGGCCGAGCTGCAGTCGCGCCTGGCCGCGCTGGGC

altered gDNA sequence snippet

TCTCCGTGGCCGAGCTGCAGGCGCGCCTGGCCGCGCTGGGC

original cDNA sequence snippet

TCTCCGTGGCCGAGCTGCAGTCGCGCCTGGCCGCGCTGGGC

altered cDNA sequence snippet

TCTCCGTGGCCGAGCTGCAGGCGCGCCTGGCCGCGCTGGGC

wildtype AA sequence

MEARFTRGKS ALLERALARP RTEVSLSAFA LLFSELVQHC QSRVFSVAEL QSRLAALGRQ
VGARVLDALV AREKGARRET KVLGALLFVK GAVWKALFGK EADKLEQAND DARTFYIIER
EPLINTYISV PKENSTLNCA SFTAGIVEAV LTHSGFPAKV TAHWHKGTTL MIKFEEAVIA
RDRALEGR*

mutated AA sequence

MEARFTRGKS ALLERALARP RTEVSLSAFA LLFSELVQHC QSRVFSVAEL QARLAALGRQ
VGARVLDALV AREKGARRET KVLGALLFVK GAVWKALFGK EADKLEQAND DARTFYIIER
EPLINTYISV PKENSTLNCA SFTAGIVEAV LTHSGFPAKV TAHWHKGTTL MIKFEEAVIA
RDRALEGR*

speed

0.19 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: 0.999991443199247 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:7747293T>GN/A show variant in all transcripts IGV

HGNC symbol

TRAPPC5

Ensembl transcript ID

ENST00000426877

Genbank transcript ID

NM_001042461

UniProt peptide

Q8IUR0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.154T>G
cDNA.315T>G
g.1533T>G

AA changes

S52A Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs6952

database	homozygous (G/G)	heterozygous	allele carriers
1000G	361	1071	1432
ExAC	2958	13135	16093

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.614	1
	1.344	1
(flanking)	1.474	0.996

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 increased	1525	wt: 0.53 / mu: 0.66	wt: CCGCGTCTTCTCCGTGGCCGAGCTGCAGTCGCGCCTGGCCG mu: CCGCGTCTTCTCCGTGGCCGAGCTGCAGGCGCGCCTGGCCG	ccga\|GCTG

distance from splice site

166

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000010400

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000040236

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000002717

Drerio

all conserved

ENSDARG00000026068

Dmelanogaster

all conserved

FBgn0033962

Celegans

not conserved

Y57A10A.16

Xtropicalis

all conserved

ENSXETG00000001289

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

567 / 567

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

189 / 189

position of stopcodon in wt / mu cDNA

728 / 728

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

162 / 162

chromosome

strand

last intron/exon boundary

150

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

567

coding sequence (CDS) position

154

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

315

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

1533

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

7747293

original gDNA sequence snippet

TCTCCGTGGCCGAGCTGCAGTCGCGCCTGGCCGCGCTGGGC

altered gDNA sequence snippet

TCTCCGTGGCCGAGCTGCAGGCGCGCCTGGCCGCGCTGGGC

original cDNA sequence snippet

TCTCCGTGGCCGAGCTGCAGTCGCGCCTGGCCGCGCTGGGC

altered cDNA sequence snippet

TCTCCGTGGCCGAGCTGCAGGCGCGCCTGGCCGCGCTGGGC

wildtype AA sequence

mutated AA sequence

speed

0.19 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems