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: ENST00000216468
Querying Taster for transcript #2: ENST00000533095
MT speed 1.92 s - this script 3.960225 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TMED8	polymorphism_automatic	5.65969493493412e-11	simple_aae		affected		Q5K	single base exchange	rs3742737		show file
SAMD15	polymorphism_automatic	0.00140073785293504	without_aae		affected			single base exchange	rs3742737		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999943403 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:77843384G>TN/A show variant in all transcripts IGV

HGNC symbol

TMED8

Ensembl transcript ID

ENST00000216468

Genbank transcript ID

NM_213601

UniProt peptide

Q6PL24

alteration type

single base exchange

alteration region

CDS

DNA changes

c.13C>A
cDNA.69C>A
g.69C>A

AA changes

Q5K Score: 53 explain score(s)

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

frameshift

known variant

Reference ID: rs3742737

database	homozygous (T/T)	heterozygous	allele carriers
1000G	182	881	1063
ExAC	70	312	382

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.663	0.01
	1.231	0.013
(flanking)	0.685	0.009

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	70	wt: 0.2240 / mu: 0.2341 (marginal change - not scored)	wt: CCTGCAGGCGGCTGA mu: CCTGAAGGCGGCTGA	TGCA\|ggcg
Donor marginally increased	74	wt: 0.8805 / mu: 0.9016 (marginal change - not scored)	wt: CAGGCGGCTGAGGGG mu: AAGGCGGCTGAGGGG	GGCG\|gctg
Donor gained	65	0.98	mu: TCTGACCTGAAGGCG	TGAC\|ctga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000006578

Mmulatta

all identical

ENSMMUG00000001098

Fcatus

no alignment

ENSFCAG00000011732

n/a

Mmusculus

all identical

ENSMUSG00000034111

Ggallus

not conserved

ENSGALG00000020410

Trubripes

no alignment

ENSTRUG00000018236

n/a

Drerio

no alignment

ENSDARG00000052390

n/a

Dmelanogaster

no alignment

FBgn0031061

n/a

Celegans

no alignment

Y41E3.7

n/a

Xtropicalis

no alignment

ENSXETG00000011082

n/a

protein features

start (aa)	end (aa)	feature	details
21	21	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
159	323	DOMAIN	GOLD.	might get lost (downstream of altered splice site)
169	169	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
242	254	COMPBIAS	Poly-Glu.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

978 / 978

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

326 / 326

position of stopcodon in wt / mu cDNA

1034 / 1034

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

57 / 57

chromosome

strand

-1

last intron/exon boundary

817

theoretical NMD boundary in CDS

710

length of CDS

978

coding sequence (CDS) position

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

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

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

77843384

original gDNA sequence snippet

GGCTGCAGATGTCTGACCTGCAGGCGGCTGAGGGGCCGGGC

altered gDNA sequence snippet

GGCTGCAGATGTCTGACCTGAAGGCGGCTGAGGGGCCGGGC

original cDNA sequence snippet

GGCTGCAGATGTCTGACCTGCAGGCGGCTGAGGGGCCGGGC

altered cDNA sequence snippet

GGCTGCAGATGTCTGACCTGAAGGCGGCTGAGGGGCCGGGC

wildtype AA sequence

MSDLQAAEGP GSWSPTARPG SAGGVGDCQG VEGSQAAASE NEDLENKDTS LLASATDPEP
CSSPHRPQMV SPVSKDATED LRKATGPLEA QALVKQDLLP ADQAQVLNEM AKYQVPQRSG
DIVMIQSEHT GAIDVLSADL ESADLLGDHR KVSPPLMAPP CIWTFAKVKE FKSKLGKEKN
SRLVVKRGEV VTIRVPTHPE GKRVCWEFAT DDYDIGFGVY FDWTPVTSTD ITVQVSDSSD
DEDEEEEEEE EIEEPVPAGD VERGSRSSLR GRYGEVMPVY RRDSHRDVQA GSHDYPGEGI
YLLKFDNSYS LLRNKTLYFH IYYTS*

mutated AA sequence

MSDLKAAEGP GSWSPTARPG SAGGVGDCQG VEGSQAAASE NEDLENKDTS LLASATDPEP
CSSPHRPQMV SPVSKDATED LRKATGPLEA QALVKQDLLP ADQAQVLNEM AKYQVPQRSG
DIVMIQSEHT GAIDVLSADL ESADLLGDHR KVSPPLMAPP CIWTFAKVKE FKSKLGKEKN
SRLVVKRGEV VTIRVPTHPE GKRVCWEFAT DDYDIGFGVY FDWTPVTSTD ITVQVSDSSD
DEDEEEEEEE EIEEPVPAGD VERGSRSSLR GRYGEVMPVY RRDSHRDVQA GSHDYPGEGI
YLLKFDNSYS LLRNKTLYFH IYYTS*

speed

0.95 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: without_aae, prob: 0.998599262147065 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:77843384G>TN/A show variant in all transcripts IGV

HGNC symbol

SAMD15

Ensembl transcript ID

ENST00000533095

Genbank transcript ID

N/A

UniProt peptide

Q9P1V8

alteration type

single base exchange

alteration region

intron

DNA changes

g.353G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3742737

database	homozygous (T/T)	heterozygous	allele carriers
1000G	182	881	1063
ExAC	70	312	382

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.663	0.01
	1.231	0.013
(flanking)	0.685	0.009

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

splice sites

splice site change before start ATG (at aa -22) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	356	wt: 0.68 / mu: 0.75	wt: CGGCCCCTCAGCCGCCTGCAGGTCAGACATCTGCAGCCCGC mu: CGGCCCCTCAGCCGCCTTCAGGTCAGACATCTGCAGCCCGC	gcag\|GTCA
Donor marginally increased	355	wt: 0.8116 / mu: 0.8525 (marginal change - not scored)	wt: CCTGCAGGTCAGACA mu: CCTTCAGGTCAGACA	TGCA\|ggtc
Acc gained	355	0.60	mu: CCGGCCCCTCAGCCGCCTTCAGGTCAGACATCTGCAGCCCG	ttca\|GGTC
Donor gained	356	0.45	mu: CTTCAGGTCAGACAT	TCAG\|gtca

distance from splice site

301

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
545	608	DOMAIN	SAM.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

122 / 122

chromosome

strand

last intron/exon boundary

152

theoretical NMD boundary in CDS

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

length of CDS

267

coding sequence (CDS) position

N/A

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

N/A

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

353

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

77843384

original gDNA sequence snippet

GCCCGGCCCCTCAGCCGCCTGCAGGTCAGACATCTGCAGCC

altered gDNA sequence snippet

GCCCGGCCCCTCAGCCGCCTTCAGGTCAGACATCTGCAGCC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MGITNFEDMK AISRHTQELL EIEEPLFKRS ISLPYRDIIG LYLEQKGHTG IKSDSLTLSE
FVKAAGLQDY APEITAPEEN EELPCTEP*

mutated AA sequence

N/A

speed

0.97 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems