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: ENST00000371325
MT speed 0 s - this script 2.176473 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FAM209B	polymorphism_automatic	4.49640324973188e-14	simple_aae		affected		Q74K	single base exchange	rs3209183		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999955 (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)

chr20:55108617C>AN/A show variant in all transcripts IGV

HGNC symbol

FAM209B

Ensembl transcript ID

ENST00000371325

Genbank transcript ID

NM_001013646

UniProt peptide

Q5JX69

alteration type

single base exchange

alteration region

CDS

DNA changes

c.220C>A
cDNA.316C>A
g.316C>A

AA changes

Q74K Score: 53 explain score(s)

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

frameshift

known variant

Reference ID: rs3209183

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1204	921	2125
ExAC	22025	-11283	10742

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.331	0.067
	0.503	0.083
(flanking)	0.525	0.092

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	319	wt: 0.9389 / mu: 0.9619 (marginal change - not scored)	wt: TGCAGTGTCAAAGAG mu: TGAAGTGTCAAAGAG	CAGT\|gtca
Donor increased	312	wt: 0.60 / mu: 0.99	wt: GTGATACTGCAGTGT mu: GTGATACTGAAGTGT	GATA\|ctgc

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 conserved

ENSPTRG00000034022

Mmulatta

all conserved

ENSMMUG00000000079

Fcatus

no alignment

ENSFCAG00000018985

n/a

Mmusculus

all conserved

ENSMUSG00000027505

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
53	73	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
74	171	TOPO_DOM	Cytoplasmic (Potential).	lost
141	141	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
143	143	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

516 / 516

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

172 / 172

position of stopcodon in wt / mu cDNA

612 / 612

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

97 / 97

chromosome

strand

last intron/exon boundary

346

theoretical NMD boundary in CDS

199

length of CDS

516

coding sequence (CDS) position

220

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

316

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

316

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

55108617

original gDNA sequence snippet

TTGTGCCGTTTGTGATACTGCAGTGTCAAAGAGACAGTGAG

altered gDNA sequence snippet

TTGTGCCGTTTGTGATACTGAAGTGTCAAAGAGACAGTGAG

original cDNA sequence snippet

TTGTGCCGTTTGTGATACTGCAGTGTCAAAGAGACAGTGAG

altered cDNA sequence snippet

TTGTGCCGTTTGTGATACTGAAGTGTCAAAGAGACAGTGAG

wildtype AA sequence

MWTLKSSLVL LLCLTCSYAF MFSSLRQKTS EPQGKVPCGE HFRIRQNLPE HTQGWLGSKW
LWLLFAVVPF VILQCQRDSE KNKEQSPPGL RGFPFRTPLK KNQNASLYKD CVFNTLNELE
VELLKFVSEV QNLKGAMATG SGSNLKLRRS EMPADPYHVT ICKIWGEESS S*

mutated AA sequence

MWTLKSSLVL LLCLTCSYAF MFSSLRQKTS EPQGKVPCGE HFRIRQNLPE HTQGWLGSKW
LWLLFAVVPF VILKCQRDSE KNKEQSPPGL RGFPFRTPLK KNQNASLYKD CVFNTLNELE
VELLKFVSEV QNLKGAMATG SGSNLKLRRS EMPADPYHVT ICKIWGEESS S*

speed

0.12 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