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: ENST00000391413
MT speed 0.37 s - this script 2.472427 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
KRTAP4-11	polymorphism_automatic	7.07709446601257e-11	simple_aae		affected		R17Q	single base exchange	rs9897031		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999929229 (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)

chr17:39274518C>TN/A show variant in all transcripts IGV

HGNC symbol

KRTAP4-11

Ensembl transcript ID

ENST00000391413

Genbank transcript ID

NM_033059

UniProt peptide

Q9BYQ6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.50G>A
cDNA.89G>A
g.89G>A

AA changes

R17Q Score: 43 explain score(s)

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

frameshift

known variant

Reference ID: rs9897031

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1293	858	2151
ExAC	29933	-27099	2834

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.418	0.195
	-0.378	0.199
(flanking)	1.665	0.282

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	85	wt: 0.80 / mu: 0.99	wt: GCTGTGGCCGAGACC mu: GCTGTGGCCAAGACC	TGTG\|gccg

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

ENSPTRG00000030937

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000069718

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
5	163	REGION	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].	lost
17	17	CONFLICT	R -> Q (in Ref. 1; CAC27583 and 3; AAI26132/AAI30563).	lost
24	28	REPEAT	2.	might get lost (downstream of altered splice site)
29	33	REPEAT	3.	might get lost (downstream of altered splice site)
34	38	REPEAT	4.	might get lost (downstream of altered splice site)
44	48	REPEAT	5.	might get lost (downstream of altered splice site)
49	53	REPEAT	6.	might get lost (downstream of altered splice site)
54	58	REPEAT	7.	might get lost (downstream of altered splice site)
59	63	REPEAT	8.	might get lost (downstream of altered splice site)
64	68	REPEAT	9.	might get lost (downstream of altered splice site)
69	73	REPEAT	10.	might get lost (downstream of altered splice site)
74	78	REPEAT	11.	might get lost (downstream of altered splice site)
79	83	REPEAT	12.	might get lost (downstream of altered splice site)
84	88	REPEAT	13.	might get lost (downstream of altered splice site)
89	93	REPEAT	14.	might get lost (downstream of altered splice site)
94	98	REPEAT	15.	might get lost (downstream of altered splice site)
99	103	REPEAT	16.	might get lost (downstream of altered splice site)
104	108	REPEAT	17.	might get lost (downstream of altered splice site)
109	113	REPEAT	18.	might get lost (downstream of altered splice site)
114	118	REPEAT	19.	might get lost (downstream of altered splice site)
119	123	REPEAT	20.	might get lost (downstream of altered splice site)
124	128	REPEAT	21.	might get lost (downstream of altered splice site)
129	133	REPEAT	22.	might get lost (downstream of altered splice site)
134	138	REPEAT	23.	might get lost (downstream of altered splice site)
144	148	REPEAT	24.	might get lost (downstream of altered splice site)
149	153	REPEAT	25.	might get lost (downstream of altered splice site)
154	158	REPEAT	26.	might get lost (downstream of altered splice site)
159	163	REPEAT	27.	might get lost (downstream of altered splice site)
167	167	CONFLICT	R -> G (in Ref. 1; CAC27583 and 3; AAI26132/AAI30563).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

588 / 588

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

196 / 196

position of stopcodon in wt / mu cDNA

627 / 627

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

40 / 40

chromosome

strand

-1

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

588

coding sequence (CDS) position

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

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

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

39274518

original gDNA sequence snippet

CTCTCACCAAGGCTGTGGCCGAGACCTCTGCCAGGAGACCT

altered gDNA sequence snippet

CTCTCACCAAGGCTGTGGCCAAGACCTCTGCCAGGAGACCT

original cDNA sequence snippet

CTCTCACCAAGGCTGTGGCCGAGACCTCTGCCAGGAGACCT

altered cDNA sequence snippet

CTCTCACCAAGGCTGTGGCCAAGACCTCTGCCAGGAGACCT

wildtype AA sequence

MVNSCCGSVC SHQGCGRDLC QETCCRPSCC ETTCCRTTYC RPSCCVSSCC RPQCCQSVCC
QPTCCRPRCC ISSCCRPSCC VSSCCKPQCC QSMCCQPTCC RPRCCISSCC RPSCCVSSCC
RPQCCQSVCC QPTCCHPSCS ISSCCRPSCC ESSCCRPCCC LRPVCGRVSC HTTCYRPTCV
ISSCPRPLCC ASSCC*

mutated AA sequence

MVNSCCGSVC SHQGCGQDLC QETCCRPSCC ETTCCRTTYC RPSCCVSSCC RPQCCQSVCC
QPTCCRPRCC ISSCCRPSCC VSSCCKPQCC QSMCCQPTCC RPRCCISSCC RPSCCVSSCC
RPQCCQSVCC QPTCCHPSCS ISSCCRPSCC ESSCCRPCCC LRPVCGRVSC HTTCYRPTCV
ISSCPRPLCC ASSCC*

speed

0.37 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