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: ENST00000380283
MT speed 0 s - this script 2.806295 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PXDC1	polymorphism_automatic	3.94106260304117e-06	simple_aae		affected		Q184H	single base exchange	rs226959		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999996058937397 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:3727811C>GN/A show variant in all transcripts IGV

HGNC symbol

PXDC1

Ensembl transcript ID

ENST00000380283

Genbank transcript ID

NM_183373

UniProt peptide

Q5TGL8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.552G>C
cDNA.1047G>C
g.24450G>C

AA changes

Q184H Score: 24 explain score(s)

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

184

frameshift

known variant

Reference ID: rs226959

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1078	1104	2182
ExAC	26486	-20205	6281

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.363	1
	0.488	0.999
(flanking)	0.873	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 increased	24453	wt: 0.30 / mu: 0.41	wt: CAGCTGGGCGTGGAC mu: CACCTGGGCGTGGAC	GCTG\|ggcg
Donor marginally increased	24441	wt: 0.9704 / mu: 0.9796 (marginal change - not scored)	wt: GGAAGAGACCAGCAG mu: GGAAGAGACCAGCAC	AAGA\|gacc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

184

mutated

not conserved

184

Ptroglodytes

not conserved

ENSPTRG00000017679

184

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000003253

Mmusculus

not conserved

ENSMUSG00000021411

184

Ggallus

not conserved

ENSGALG00000012814

184

Trubripes

not conserved

ENSTRUG00000008605

184

Drerio

not conserved

ENSDARG00000040309

182

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000018024

184

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

696 / 696

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

232 / 232

position of stopcodon in wt / mu cDNA

1191 / 1191

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

496 / 496

chromosome

strand

-1

last intron/exon boundary

1074

theoretical NMD boundary in CDS

528

length of CDS

696

coding sequence (CDS) position

552

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

1047

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

24450

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

3727811

original gDNA sequence snippet

CCAAATGGAAGAGACCAGCAGCTGGGCGTGGACCCAACAGA

altered gDNA sequence snippet

CCAAATGGAAGAGACCAGCACCTGGGCGTGGACCCAACAGA

original cDNA sequence snippet

CCAAATGGAAGAGACCAGCAGCTGGGCGTGGACCCAACAGA

altered cDNA sequence snippet

CCAAATGGAAGAGACCAGCACCTGGGCGTGGACCCAACAGA

wildtype AA sequence

MASAVFEGTS LVNMFVRGCW VNGIRRLIVS RRGDEEEFFE IRTEWSDRSV LYLHRSLADL
GRLWQRLRDA FPEDRSELAQ GPLRQGLVAI KEAHDIETRL NEVEKLLKTI ISMPCKYSRS
EVVLTFFERS PLDQVLKNDN VHKIQPSFQS PVKISEIMRS NGFCLANTET IVIDHSIPNG
RDQQLGVDPT EHLFENGSEF PSELEDGDDP AAYVTNLSYY HLVPFETDIW D*

mutated AA sequence

MASAVFEGTS LVNMFVRGCW VNGIRRLIVS RRGDEEEFFE IRTEWSDRSV LYLHRSLADL
GRLWQRLRDA FPEDRSELAQ GPLRQGLVAI KEAHDIETRL NEVEKLLKTI ISMPCKYSRS
EVVLTFFERS PLDQVLKNDN VHKIQPSFQS PVKISEIMRS NGFCLANTET IVIDHSIPNG
RDQHLGVDPT EHLFENGSEF PSELEDGDDP AAYVTNLSYY HLVPFETDIW D*

speed

0.80 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