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: ENST00000230588
MT speed 0 s - this script 2.469391 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MEP1A	polymorphism_automatic	1.16795462190566e-12	simple_aae		affected		T606S	single base exchange	rs2297020		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998832 (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)

chr6:46803018A>TN/A show variant in all transcripts IGV

HGNC symbol

MEP1A

Ensembl transcript ID

ENST00000230588

Genbank transcript ID

NM_005588

UniProt peptide

Q16819

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1816A>T
cDNA.1825A>T
g.41892A>T

AA changes

T606S Score: 58 explain score(s)

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

606

frameshift

known variant

Reference ID: rs2297020

database	homozygous (T/T)	heterozygous	allele carriers
1000G	266	1089	1355
ExAC	3675	19935	23610

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.598	0
	-0.963	0
(flanking)	-0.012	0

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 gained	41896	0.48	mu: CCAGACTGAAGTTCCCTCTAAAGGCAAAAGACTGAGCCCCC	ctaa\|AGGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

606

mutated

all conserved

606

Ptroglodytes

all identical

ENSPTRG00000018239

606

Mmulatta

all identical

ENSMMUG00000023000

606

Fcatus

not conserved

ENSFCAG00000009298

560

Mmusculus

not conserved

ENSMUSG00000023914

620

Ggallus

not conserved

ENSGALG00000016715

607

Trubripes

not conserved

ENSTRUG00000004892

427

KPAEP

Drerio

all identical

ENSDARG00000008029

591

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000016251

608

protein features

start (aa)	end (aa)	feature	details
66	712	TOPO_DOM	Extracellular (Potential).	lost
638	638	CONFLICT	A -> V (in Ref. 3; BAF98731).	might get lost (downstream of altered splice site)
670	710	DOMAIN	EGF-like.	might get lost (downstream of altered splice site)
674	674	DISULFID	By similarity.	might get lost (downstream of altered splice site)
679	679	DISULFID	By similarity.	might get lost (downstream of altered splice site)
685	685	DISULFID	By similarity.	might get lost (downstream of altered splice site)
694	694	DISULFID	By similarity.	might get lost (downstream of altered splice site)
696	696	DISULFID	By similarity.	might get lost (downstream of altered splice site)
709	709	DISULFID	By similarity.	might get lost (downstream of altered splice site)
711	713	CONFLICT	AVQ -> SAE (in Ref. 1; AAA21338 and 7; no nucleotide entry).	might get lost (downstream of altered splice site)
713	740	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
741	746	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2241 / 2241

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

747 / 747

position of stopcodon in wt / mu cDNA

2250 / 2250

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

10 / 10

chromosome

strand

last intron/exon boundary

2094

theoretical NMD boundary in CDS

2034

length of CDS

2241

coding sequence (CDS) position

1816

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

1825

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

41892

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

46803018

original gDNA sequence snippet

TCAGCCAGACTGAAGTTCCCACTAAAGGCAAAAGACTGAGC

altered gDNA sequence snippet

TCAGCCAGACTGAAGTTCCCTCTAAAGGCAAAAGACTGAGC

original cDNA sequence snippet

TCAGCCAGACTGAAGTTCCCACTAAAGGCAAAAGACTGAGC

altered cDNA sequence snippet

TCAGCCAGACTGAAGTTCCCTCTAAAGGCAAAAGACTGAGC

wildtype AA sequence

MAWIRSTCIL FFTLLFAHIA AVPIKYLPEE NVHDADFGEQ KDISEINLAA GLDLFQGDIL
LQKSRNGLRD PNTRWTFPIP YILADNLGLN AKGAILYAFE MFRLKSCVDF KPYEGESSYI
IFQQFDGCWS EVGDQHVGQN ISIGQGCAYK AIIEHEILHA LGFYHEQSRT DRDDYVNIWW
DQILSGYQHN FDTYDDSLIT DLNTPYDYES LMHYQPFSFN KNASVPTITA KIPEFNSIIG
QRLDFSAIDL ERLNRMYNCT TTHTLLDHCT FEKANICGMI QGTRDDTDWA HQDSAQAGEV
DHTLLGQCTG AGYFMQFSTS SGSAEEAALL ESRILYPKRK QQCLQFFYKM TGSPSDRLVV
WVRRDDSTGN VRKLVKVQTF QGDDDHNWKI AHVVLKEEQK FRYLFQGTKG DPQNSTGGIY
LDDITLTETP CPTGVWTVRN FSQVLENTSK GDKLQSPRFY NSEGYGFGVT LYPNSRESSG
YLRLAFHVCS GENDAILEWP VENRQVIITI LDQEPDVRNR MSSSMVFTTS KSHTSPAIND
TVIWDRPSRV GTYHTDCNCF RSIDLGWSGF ISHQMLKRRS FLKNDDLIIF VDFEDITHLS
QTEVPTKGKR LSPQGLILQG QEQQVSEEGS GKAMLEEALP VSLSQGQPSR QKRSVENTGP
LEDHNWPQYF RDPCDPNPCQ NDGICVNVKG MASCRCISGH AFFYTGERCQ AVQVHGSVLG
MVIGGTAGVI FLTFSIIAIL SQRPRK*

mutated AA sequence

MAWIRSTCIL FFTLLFAHIA AVPIKYLPEE NVHDADFGEQ KDISEINLAA GLDLFQGDIL
LQKSRNGLRD PNTRWTFPIP YILADNLGLN AKGAILYAFE MFRLKSCVDF KPYEGESSYI
IFQQFDGCWS EVGDQHVGQN ISIGQGCAYK AIIEHEILHA LGFYHEQSRT DRDDYVNIWW
DQILSGYQHN FDTYDDSLIT DLNTPYDYES LMHYQPFSFN KNASVPTITA KIPEFNSIIG
QRLDFSAIDL ERLNRMYNCT TTHTLLDHCT FEKANICGMI QGTRDDTDWA HQDSAQAGEV
DHTLLGQCTG AGYFMQFSTS SGSAEEAALL ESRILYPKRK QQCLQFFYKM TGSPSDRLVV
WVRRDDSTGN VRKLVKVQTF QGDDDHNWKI AHVVLKEEQK FRYLFQGTKG DPQNSTGGIY
LDDITLTETP CPTGVWTVRN FSQVLENTSK GDKLQSPRFY NSEGYGFGVT LYPNSRESSG
YLRLAFHVCS GENDAILEWP VENRQVIITI LDQEPDVRNR MSSSMVFTTS KSHTSPAIND
TVIWDRPSRV GTYHTDCNCF RSIDLGWSGF ISHQMLKRRS FLKNDDLIIF VDFEDITHLS
QTEVPSKGKR LSPQGLILQG QEQQVSEEGS GKAMLEEALP VSLSQGQPSR QKRSVENTGP
LEDHNWPQYF RDPCDPNPCQ NDGICVNVKG MASCRCISGH AFFYTGERCQ AVQVHGSVLG
MVIGGTAGVI FLTFSIIAIL SQRPRK*

speed

0.23 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