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: ENST00000255008
MT speed 0 s - this script 2.735161 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SSTR4	polymorphism_automatic	1.0902390101819e-13	simple_aae		affected		F321S	single base exchange	rs2567608		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999891 (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)

chr20:23017082T>CN/A show variant in all transcripts IGV

HGNC symbol

SSTR4

Ensembl transcript ID

ENST00000255008

Genbank transcript ID

NM_001052

UniProt peptide

P31391

alteration type

single base exchange

alteration region

CDS

DNA changes

c.962T>C
cDNA.1026T>C
g.1026T>C

AA changes

F321S Score: 155 explain score(s)

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

321

frameshift

known variant

Reference ID: rs2567608

database	homozygous (C/C)	heterozygous	allele carriers
1000G	707	1188	1895
ExAC	14360	4047	18407

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.973	0.02
	1.585	0.025
(flanking)	-1.368	0.015

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 marginally increased	1019	wt: 0.7276 / mu: 0.7341 (marginal change - not scored)	wt: GCTTCCTCTCCGACAACTTCCGCCGATTCTTCCAGCGGGTT mu: GCTTCCTCTCCGACAACTTCCGCCGATCCTTCCAGCGGGTT	ttcc\|GCCG
Acc increased	1023	wt: 0.54 / mu: 0.60	wt: CCTCTCCGACAACTTCCGCCGATTCTTCCAGCGGGTTCTCT mu: CCTCTCCGACAACTTCCGCCGATCCTTCCAGCGGGTTCTCT	gccg\|ATTC
Acc marginally increased	1027	wt: 0.2182 / mu: 0.2358 (marginal change - not scored)	wt: TCCGACAACTTCCGCCGATTCTTCCAGCGGGTTCTCTGCCT mu: TCCGACAACTTCCGCCGATCCTTCCAGCGGGTTCTCTGCCT	attc\|TTCC

distance from splice site

233

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

321

mutated

not conserved

321

Ptroglodytes

not conserved

ENSPTRG00000013316

321

Mmulatta

not conserved

ENSMMUG00000016815

321

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000037014

318

Ggallus

not conserved

ENSGALG00000008362

316

LRRCLDA

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000031664

314

protein features

start (aa)	end (aa)	feature	details
315	388	TOPO_DOM	Cytoplasmic (Potential).	lost
327	327	LIPID	S-palmitoyl cysteine (Potential).	might get lost (downstream of altered splice site)
365	365	CONFLICT	P -> K (in Ref. 2; AAA60565).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1167 / 1167

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

389 / 389

position of stopcodon in wt / mu cDNA

1231 / 1231

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

65 / 65

chromosome

strand

last intron/exon boundary

theoretical NMD boundary in CDS

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

length of CDS

1167

coding sequence (CDS) position

962

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

1026

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

1026

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

23017082

original gDNA sequence snippet

CTCCGACAACTTCCGCCGATTCTTCCAGCGGGTTCTCTGCC

altered gDNA sequence snippet

CTCCGACAACTTCCGCCGATCCTTCCAGCGGGTTCTCTGCC

original cDNA sequence snippet

CTCCGACAACTTCCGCCGATTCTTCCAGCGGGTTCTCTGCC

altered cDNA sequence snippet

CTCCGACAACTTCCGCCGATCCTTCCAGCGGGTTCTCTGCC

wildtype AA sequence

MSAPSTLPPG GEEGLGTAWP SAANASSAPA EAEEAVAGPG DARAAGMVAI QCIYALVCLV
GLVGNALVIF VILRYAKMKT ATNIYLLNLA VADELFMLSV PFVASSAALR HWPFGSVLCR
AVLSVDGLNM FTSVFCLTVL SVDRYVAVVH PLRAATYRRP SVAKLINLGV WLASLLVTLP
IAIFADTRPA RGGQAVACNL QWPHPAWSAV FVVYTFLLGF LLPVLAIGLC YLLIVGKMRA
VALRAGWQQR RRSEKKITRL VLMVVVVFVL CWMPFYVVQL LNLFVTSLDA TVNHVSLILS
YANSCANPIL YGFLSDNFRR FFQRVLCLRC CLLEGAGGAE EEPLDYYATA LKSKGGAGCM
CPPLPCQQEA LQPEPGRKRI PLTRTTTF*

mutated AA sequence

MSAPSTLPPG GEEGLGTAWP SAANASSAPA EAEEAVAGPG DARAAGMVAI QCIYALVCLV
GLVGNALVIF VILRYAKMKT ATNIYLLNLA VADELFMLSV PFVASSAALR HWPFGSVLCR
AVLSVDGLNM FTSVFCLTVL SVDRYVAVVH PLRAATYRRP SVAKLINLGV WLASLLVTLP
IAIFADTRPA RGGQAVACNL QWPHPAWSAV FVVYTFLLGF LLPVLAIGLC YLLIVGKMRA
VALRAGWQQR RRSEKKITRL VLMVVVVFVL CWMPFYVVQL LNLFVTSLDA TVNHVSLILS
YANSCANPIL YGFLSDNFRR SFQRVLCLRC CLLEGAGGAE EEPLDYYATA LKSKGGAGCM
CPPLPCQQEA LQPEPGRKRI PLTRTTTF*

speed

0.73 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