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: ENST00000321731
MT speed 0 s - this script 2.328168 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C14orf39	polymorphism_automatic	1.61108419960421e-05	simple_aae				L524F	single base exchange	rs1254319		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999983889158004 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM140045)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:60903757G>AN/A show variant in all transcripts IGV

HGNC symbol

C14orf39

Ensembl transcript ID

ENST00000321731

Genbank transcript ID

NM_174978

UniProt peptide

Q8N1H7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1570C>T
cDNA.1730C>T
g.78505C>T

AA changes

L524F Score: 22 explain score(s)

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

524

frameshift

known variant

Reference ID: rs1254319

database	homozygous (A/A)	heterozygous	allele carriers
1000G	609	1120	1729
ExAC	8790	15187	23977

known disease mutation at this position, please check HGMD for details (HGMD ID CM140045)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.216	1
	1.134	1
(flanking)	0.233	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
Acc marginally increased	78495	wt: 0.9730 / mu: 0.9782 (marginal change - not scored)	wt: TTGTAATGTTTATCTTCCTTAGGAAACTTACTTGAGAAGCC mu: TTGTAATGTTTATCTTCCTTAGGAAACTTATTTGAGAAGCC	ctta\|GGAA
Acc marginally increased	78496	wt: 0.9623 / mu: 0.9626 (marginal change - not scored)	wt: TGTAATGTTTATCTTCCTTAGGAAACTTACTTGAGAAGCCA mu: TGTAATGTTTATCTTCCTTAGGAAACTTATTTGAGAAGCCA	ttag\|GAAA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

524

mutated

not conserved

524

Ptroglodytes

not conserved

ENSPTRG00000006408

524

Mmulatta

not conserved

ENSMMUG00000002828

522

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021098

514

Ggallus

not conserved

ENSGALG00000020358

518

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
524	524	CONFLICT	L -> F (in Ref. 1; BAC05253).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1764 / 1764

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

588 / 588

position of stopcodon in wt / mu cDNA

1924 / 1924

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

161 / 161

chromosome

strand

-1

last intron/exon boundary

1722

theoretical NMD boundary in CDS

1511

length of CDS

1764

coding sequence (CDS) position

1570

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

1730

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

78505

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

60903757

original gDNA sequence snippet

TATCTTCCTTAGGAAACTTACTTGAGAAGCCAGAAGGAGAA

altered gDNA sequence snippet

TATCTTCCTTAGGAAACTTATTTGAGAAGCCAGAAGGAGAA

original cDNA sequence snippet

AGCAAGAGATTGGAAACTTACTTGAGAAGCCAGAAGGAGAA

altered cDNA sequence snippet

AGCAAGAGATTGGAAACTTATTTGAGAAGCCAGAAGGAGAA

wildtype AA sequence

MNDSLFVSLD RLLLEFVFQY EQDISTKEEM IQRINKCCED IKENKVTICR IHETINATDE
EIDHYCKHSE EIKDNCRNWK PTCDVFRKHE DYMQDQFTVY QGTVEKDKEM YHDYICQYKE
VLKQYQLKYS ETPFSREYYE KKREHEEIQS RVLACTEQLK MNETIFMKFR VPAPFPSLTK
WTLNIVNLRC ETQDILKHAS NLTKSSSELK KEVDEMEIEI NYLNQQISRH NETKALSETL
EEKNKNTENR KELKERIFGK DEHVLTLNKT QSSQLFLPYE SQKLVRPIKM HSSEPRVADI
KEESSAKQSK LANIDFRQKE NDTQIFNDSA VDNHSKCSHI TTITSSQKFM QVRLLTPQKQ
SNSNQWSEKG DKDAEYGDKG TVRQVRESKC TSQAIYTEHF GKSVENDSDE VEERAENFPR
TSEIPIFLGT PKAVKAPESL EKIKFPKTPP FEINRNRNAV PEVQTEKESP GLSFLMSYTS
RSPGLNLFDS SVFDTEISSD QFNEHYSARN LNPLSSEQEI GNLLEKPEGE DGFTFSFPSD
TSTHTFGAGK DDFSFPFSFG QGQNSIPSSS LKGFSSSSQN TTQFTFF*

mutated AA sequence

MNDSLFVSLD RLLLEFVFQY EQDISTKEEM IQRINKCCED IKENKVTICR IHETINATDE
EIDHYCKHSE EIKDNCRNWK PTCDVFRKHE DYMQDQFTVY QGTVEKDKEM YHDYICQYKE
VLKQYQLKYS ETPFSREYYE KKREHEEIQS RVLACTEQLK MNETIFMKFR VPAPFPSLTK
WTLNIVNLRC ETQDILKHAS NLTKSSSELK KEVDEMEIEI NYLNQQISRH NETKALSETL
EEKNKNTENR KELKERIFGK DEHVLTLNKT QSSQLFLPYE SQKLVRPIKM HSSEPRVADI
KEESSAKQSK LANIDFRQKE NDTQIFNDSA VDNHSKCSHI TTITSSQKFM QVRLLTPQKQ
SNSNQWSEKG DKDAEYGDKG TVRQVRESKC TSQAIYTEHF GKSVENDSDE VEERAENFPR
TSEIPIFLGT PKAVKAPESL EKIKFPKTPP FEINRNRNAV PEVQTEKESP GLSFLMSYTS
RSPGLNLFDS SVFDTEISSD QFNEHYSARN LNPLSSEQEI GNLFEKPEGE DGFTFSFPSD
TSTHTFGAGK DDFSFPFSFG QGQNSIPSSS LKGFSSSSQN TTQFTFF*

speed

0.32 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