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: ENST00000331428
MT speed 0 s - this script 3.025825 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
XKR3	polymorphism_automatic	1.60982338570648e-13	simple_aae		affected		H442N	single base exchange	rs5748622		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999839 (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)

chr22:17264565G>TN/A show variant in all transcripts IGV

HGNC symbol

XKR3

Ensembl transcript ID

ENST00000331428

Genbank transcript ID

NM_175878

UniProt peptide

Q5GH77

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1324C>A
cDNA.1427C>A
g.38025C>A

AA changes

H442N Score: 68 explain score(s)

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

442

frameshift

known variant

Reference ID: rs5748622

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1341	564	1905
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.251	0
	-0.107	0.001
(flanking)	0.645	0.002

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	38022	wt: 0.6807 / mu: 0.6989 (marginal change - not scored)	wt: ATTACTGTCACTCCT mu: ATTACTGTAACTCCT	TACT\|gtca
Donor gained	38021	0.53	mu: AATTACTGTAACTCC	TTAC\|tgta

distance from splice site

264

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

442

mutated

all conserved

442

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no alignment

ENSGALG00000006637

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000044011

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000009649

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1380 / 1380

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

460 / 460

position of stopcodon in wt / mu cDNA

1483 / 1483

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

104 / 104

chromosome

strand

-1

last intron/exon boundary

693

theoretical NMD boundary in CDS

539

length of CDS

1380

coding sequence (CDS) position

1324

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

1427

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

38025

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

17264565

original gDNA sequence snippet

AGCAGCTGAGGAATTACTGTCACTCCTGCAATAGGGTTGGA

altered gDNA sequence snippet

AGCAGCTGAGGAATTACTGTAACTCCTGCAATAGGGTTGGA

original cDNA sequence snippet

AGCAGCTGAGGAATTACTGTCACTCCTGCAATAGGGTTGGA

altered cDNA sequence snippet

AGCAGCTGAGGAATTACTGTAACTCCTGCAATAGGGTTGGA

wildtype AA sequence

METVFEEMDE ESTGGVSSSK EEIVLGQRLH LSFPFSIIFS TVLYCGEVAF GLYMFEIYRK
ANDTFWMSFT ISFIIVGAIL DQIILMFFNK DLRRNKAALL FWHILLLGPI VRCLHTIRNY
HKWLKNLKQE KEETQVSITK RNTMLEREIA FSIRDNFMQQ KAFKYMSVIQ AFLGSVPQLI
LQMYISLTIR EWPLNRALLM TFSLLSVTYG AIRCNILAIQ ISNDDTTIKL PPIEFFCVVM
WRFLEVISRV VTLAFFIASL KLKSLPVLLI IYFVSLLAPW LEFWKSGAHL PGNKENNSNM
VGTVLMLFLI TLLYAAINFS CWSAVKLQLS DDKIIDGRQR WGHRILHYSF QFLENVIMIL
VFRFFGGKTL LNCCDSLIAV QLIISYLLAT GFMLLFYQYL YPWQSGKVLP GRTENQPEAP
YYYVNIEKTE KNKNKQLRNY CHSCNRVGYF SIRKSMTCS*

mutated AA sequence

speed

1.02 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