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: ENST00000231656
MT speed 0.57 s - this script 2.635679 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CDX1	polymorphism_automatic	1.02382524099776e-05	simple_aae		affected		P130R	single base exchange	rs2302275		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99998976174759 (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)

chr5:149546828C>GN/A show variant in all transcripts IGV

HGNC symbol

CDX1

Ensembl transcript ID

ENST00000231656

Genbank transcript ID

NM_001804

UniProt peptide

P47902

alteration type

single base exchange

alteration region

CDS

DNA changes

c.389C>G
cDNA.470C>G
g.470C>G

AA changes

P130R Score: 103 explain score(s)

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

130

frameshift

known variant

Reference ID: rs2302275

database	homozygous (G/G)	heterozygous	allele carriers
1000G	896	1085	1981
ExAC	146	166	312

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.387	1
	1.591	1
(flanking)	0.955	1

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	461	wt: 0.9721 / mu: 0.9786 (marginal change - not scored)	wt: CGGAGCGCAGAGGCC mu: CGGAGCGCAGAGGCG	GAGC\|gcag
Donor increased	464	wt: 0.40 / mu: 0.99	wt: AGCGCAGAGGCCGAC mu: AGCGCAGAGGCGGAC	CGCA\|gagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

130

mutated

not conserved

130

Ptroglodytes

not conserved

ENSPTRG00000017411

130

Mmulatta

not conserved

ENSMMUG00000011558

130

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000024619

130

Ggallus

not conserved

ENSGALG00000005679

115

Trubripes

not conserved

ENSTRUG00000000997

150

Drerio

not conserved

ENSDARG00000058999

124

Dmelanogaster

no homologue

Celegans

no alignment

C38D4.6

n/a

Xtropicalis

not conserved

ENSXETG00000010282

125

protein features

start (aa)	end (aa)	feature	details
143	149	COMPBIAS	Poly-Gly.	might get lost (downstream of altered splice site)
154	213	DNA_BIND	Homeobox.	might get lost (downstream of altered splice site)
217	221	COMPBIAS	Poly-Gln.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

798 / 798

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

266 / 266

position of stopcodon in wt / mu cDNA

879 / 879

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

82 / 82

chromosome

strand

last intron/exon boundary

673

theoretical NMD boundary in CDS

541

length of CDS

798

coding sequence (CDS) position

389

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

470

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

470

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

149546828

original gDNA sequence snippet

CTCGCCCGGAGCGCAGAGGCCGACGCCCTACGAGTGGATGC

altered gDNA sequence snippet

CTCGCCCGGAGCGCAGAGGCGGACGCCCTACGAGTGGATGC

original cDNA sequence snippet

CTCGCCCGGAGCGCAGAGGCCGACGCCCTACGAGTGGATGC

altered cDNA sequence snippet

CTCGCCCGGAGCGCAGAGGCGGACGCCCTACGAGTGGATGC

wildtype AA sequence

MYVGYVLDKD SPVYPGPARP ASLGLGPQAY GPPAPPPAPP QYPDFSSYSH VEPAPAPPTA
WGAPFPAPKD DWAAAYGPGP AAPAASPASL AFGPPPDFSP VPAPPGPGPG LLAQPLGGPG
TPSSPGAQRP TPYEWMRRSV AAGGGGGSGK TRTKDKYRVV YTDHQRLELE KEFHYSRYIT
IRRKSELAAN LGLTERQVKI WFQNRRAKER KVNKKKQQQQ QPPQPPMAHD ITATPAGPSL
GGLCPSNTSL LATSSPMPVK EEFLP*

mutated AA sequence

MYVGYVLDKD SPVYPGPARP ASLGLGPQAY GPPAPPPAPP QYPDFSSYSH VEPAPAPPTA
WGAPFPAPKD DWAAAYGPGP AAPAASPASL AFGPPPDFSP VPAPPGPGPG LLAQPLGGPG
TPSSPGAQRR TPYEWMRRSV AAGGGGGSGK TRTKDKYRVV YTDHQRLELE KEFHYSRYIT
IRRKSELAAN LGLTERQVKI WFQNRRAKER KVNKKKQQQQ QPPQPPMAHD ITATPAGPSL
GGLCPSNTSL LATSSPMPVK EEFLP*

speed

0.57 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