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: ENST00000251643
MT speed 0.83 s - this script 3.00515 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
KRT12	polymorphism_automatic	1.87969639853236e-11	simple_aae				P15S	single base exchange	rs11650915		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999981203 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:39023396G>AN/A show variant in all transcripts IGV

HGNC symbol

KRT12

Ensembl transcript ID

ENST00000251643

Genbank transcript ID

NM_000223

UniProt peptide

Q99456

alteration type

single base exchange

alteration region

CDS

DNA changes

c.43C>T
cDNA.67C>T
g.67C>T

AA changes

P15S Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs11650915

database	homozygous (A/A)	heterozygous	allele carriers
1000G	320	910	1230
ExAC	8288	16191	24479

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.335	0.008
	0.48	0.007
(flanking)	1.105	0.006

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
Acc marginally increased	70	wt: 0.5272 / mu: 0.5723 (marginal change - not scored)	wt: CACTCTCAGTGCGCACCCCCGGACTGTCCCGGCGGCTCTCC mu: CACTCTCAGTGCGCACCTCCGGACTGTCCCGGCGGCTCTCC	cccg\|GACT
Acc marginally increased	57	wt: 0.7410 / mu: 0.7874 (marginal change - not scored)	wt: AACAACACCATGTCACTCTCAGTGCGCACCCCCGGACTGTC mu: AACAACACCATGTCACTCTCAGTGCGCACCTCCGGACTGTC	ctca\|GTGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000009134

Mmulatta

all identical

ENSMMUG00000001502

Fcatus

not conserved

ENSFCAG00000002020

Mmusculus

not conserved

ENSMUSG00000020912

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000025341

n/a

protein features

start (aa)	end (aa)	feature	details
1	124	REGION	Head.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1485 / 1485

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

495 / 495

position of stopcodon in wt / mu cDNA

1509 / 1509

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

25 / 25

chromosome

strand

-1

last intron/exon boundary

1412

theoretical NMD boundary in CDS

1337

length of CDS

1485

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)

39023396

original gDNA sequence snippet

TGTCACTCTCAGTGCGCACCCCCGGACTGTCCCGGCGGCTC

altered gDNA sequence snippet

TGTCACTCTCAGTGCGCACCTCCGGACTGTCCCGGCGGCTC

original cDNA sequence snippet

TGTCACTCTCAGTGCGCACCCCCGGACTGTCCCGGCGGCTC

altered cDNA sequence snippet

TGTCACTCTCAGTGCGCACCTCCGGACTGTCCCGGCGGCTC

wildtype AA sequence

MDLSNNTMSL SVRTPGLSRR LSSQSVIGRP RGMSASSVGS GYGGSAFGFG ASCGGGFSAA
SMFGSSSGFG GGSGSSMAGG LGAGYGRALG GGSFGGLGMG FGGSPGGGSL GILSGNDGGL
LSGSEKETMQ NLNDRLASYL DKVRALEEAN TELENKIREW YETRGTGTAD ASQSDYSKYY
PLIEDLRNKI ISASIGNAQL LLQIDNARLA AEDFRMKYEN ELALRQGVEA DINGLRRVLD
ELTLTRTDLE MQIESLNEEL AYMKKNHEDE LQSFRVGGPG EVSVEMDAAP GVDLTRLLND
MRAQYETIAE QNRKDAEAWF IEKSGELRKE ISTNTEQLQS SKSEVTDLRR AFQNLEIELQ
SQLAMKKSLE DSLAEAEGDY CAQLSQVQQL ISNLEAQLLQ VRADAERQNV DHQRLLNVKA
RLELEIETYR RLLDGEAQGD GLEESLFVTD SKSQAQSTDS SKDPTKTRKI KTVVQEMVNG
EVVSSQVQEI EELM*

mutated AA sequence

MDLSNNTMSL SVRTSGLSRR LSSQSVIGRP RGMSASSVGS GYGGSAFGFG ASCGGGFSAA
SMFGSSSGFG GGSGSSMAGG LGAGYGRALG GGSFGGLGMG FGGSPGGGSL GILSGNDGGL
LSGSEKETMQ NLNDRLASYL DKVRALEEAN TELENKIREW YETRGTGTAD ASQSDYSKYY
PLIEDLRNKI ISASIGNAQL LLQIDNARLA AEDFRMKYEN ELALRQGVEA DINGLRRVLD
ELTLTRTDLE MQIESLNEEL AYMKKNHEDE LQSFRVGGPG EVSVEMDAAP GVDLTRLLND
MRAQYETIAE QNRKDAEAWF IEKSGELRKE ISTNTEQLQS SKSEVTDLRR AFQNLEIELQ
SQLAMKKSLE DSLAEAEGDY CAQLSQVQQL ISNLEAQLLQ VRADAERQNV DHQRLLNVKA
RLELEIETYR RLLDGEAQGD GLEESLFVTD SKSQAQSTDS SKDPTKTRKI KTVVQEMVNG
EVVSSQVQEI EELM*

speed

0.83 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