MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000297819
MT speed 0 s - this script 2.822655 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SSMEM1	polymorphism_automatic	2.80710010791552e-10	simple_aae				R88W	single base exchange	rs4728190		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999971929 (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)

chr7:129855837C>TN/A show variant in all transcripts IGV

HGNC symbol

SSMEM1

Ensembl transcript ID

ENST00000297819

Genbank transcript ID

NM_145268

UniProt peptide

Q8WWF3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.262C>T
cDNA.313C>T
g.8138C>T

AA changes

R88W Score: 101 explain score(s)

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

frameshift

known variant

Reference ID: rs4728190

database	homozygous (T/T)	heterozygous	allele carriers
1000G	133	670	803
ExAC	3313	19755	23068

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.728	0.013
	-0.55	0
(flanking)	0.866	0.001

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	8136	wt: 0.5824 / mu: 0.5847 (marginal change - not scored)	wt: CTGTAAGCGGCAAAG mu: CTGTAAGTGGCAAAG	GTAA\|gcgg
Donor marginally increased	8131	wt: 0.9065 / mu: 0.9160 (marginal change - not scored)	wt: ACTTCCTGTAAGCGG mu: ACTTCCTGTAAGTGG	TTCC\|tgta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000019692

Mmulatta

not conserved

ENSMMUG00000010060

Fcatus

all identical

ENSFCAG00000009319

Mmusculus

all identical

ENSMUSG00000029784

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

735 / 735

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

245 / 245

position of stopcodon in wt / mu cDNA

786 / 786

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

52 / 52

chromosome

strand

last intron/exon boundary

290

theoretical NMD boundary in CDS

188

length of CDS

735

coding sequence (CDS) position

262

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

313

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

8138

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

129855837

original gDNA sequence snippet

GCAAAGAGACTTCCTGTAAGCGGCAAAGCAAAGACAGTGCC

altered gDNA sequence snippet

GCAAAGAGACTTCCTGTAAGTGGCAAAGCAAAGACAGTGCC

original cDNA sequence snippet

GCAAAGAGACTTCCTGTAAGCGGCAAAGCAAAGACAGTGCC

altered cDNA sequence snippet

GCAAAGAGACTTCCTGTAAGTGGCAAAGCAAAGACAGTGCC

wildtype AA sequence

MGDLFSLFWE VDPPPIPVNC AIPNQDYECW KDDSCGTIGS FLLWYFVIVF VLMFFSRASV
WMSEDKKDEG SGTSTSVRKA SKETSCKRQS KDSAWDPSQT MKKPKQNQLT PVTNSEVALV
NAYPEQRRAR RQSQFNEVNQ NQHDSDTTEY GSEESNSEAS SWKESESEHH PSPDSIKRRK
MAQRQRNLGS YQMSERHCLH CKALRTNEWL AHHSRQKPSV TPPMKRDSQE ESSISDINKK
FSKF*

mutated AA sequence

MGDLFSLFWE VDPPPIPVNC AIPNQDYECW KDDSCGTIGS FLLWYFVIVF VLMFFSRASV
WMSEDKKDEG SGTSTSVRKA SKETSCKWQS KDSAWDPSQT MKKPKQNQLT PVTNSEVALV
NAYPEQRRAR RQSQFNEVNQ NQHDSDTTEY GSEESNSEAS SWKESESEHH PSPDSIKRRK
MAQRQRNLGS YQMSERHCLH CKALRTNEWL AHHSRQKPSV TPPMKRDSQE ESSISDINKK
FSKF*

speed

0.81 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems