MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000392328
Querying Taster for transcript #2: ENST00000281416
MT speed 0 s - this script 3.053033 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MFSD6	polymorphism_automatic	4.23994173104347e-13	simple_aae				R205G	single base exchange	rs9646748		show file
MFSD6	polymorphism_automatic	4.23994173104347e-13	simple_aae				R205G	single base exchange	rs9646748		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999576 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:191301368A>GN/A show variant in all transcripts IGV

HGNC symbol

MFSD6

Ensembl transcript ID

ENST00000392328

Genbank transcript ID

NM_017694

UniProt peptide

Q6ZSS7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.613A>G
cDNA.937A>G
g.28288A>G

AA changes

R205G Score: 125 explain score(s)

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

205

frameshift

known variant

Reference ID: rs9646748

database	homozygous (G/G)	heterozygous	allele carriers
1000G	659	1148	1807
ExAC	15029	2709	17738

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.563	0
	2.072	0.006
(flanking)	-0.458	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

666

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

205

mutated

not conserved

205

Ptroglodytes

not conserved

ENSPTRG00000012743

205

Mmulatta

not conserved

ENSMMUG00000007289

205

Fcatus

not conserved

ENSFCAG00000005191

201

Mmusculus

not conserved

ENSMUSG00000041439

206

DVQ

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000032318

207

IGQYPWRTILSSGQSSGYIS

Dmelanogaster

not conserved

FBgn0033958

232

Celegans

not conserved

R13A5.9

154

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2376 / 2376

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

792 / 792

position of stopcodon in wt / mu cDNA

2700 / 2700

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

325 / 325

chromosome

strand

last intron/exon boundary

2497

theoretical NMD boundary in CDS

2122

length of CDS

2376

coding sequence (CDS) position

613

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

937

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

28288

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

191301368

original gDNA sequence snippet

AAAGAAACCTTTTGGAAACAAGGCTCAATGTCTCAGACACC

altered gDNA sequence snippet

AAAGAAACCTTTTGGAAACAGGGCTCAATGTCTCAGACACC

original cDNA sequence snippet

AAAGAAACCTTTTGGAAACAAGGCTCAATGTCTCAGACACC

altered cDNA sequence snippet

AAAGAAACCTTTTGGAAACAGGGCTCAATGTCTCAGACACC

wildtype AA sequence

MADDKVAILT DDEEEQKRKY VLADPFNGIS REPEPPSNET PSSTETSAIP EEEIDWIEKH
CVKINNDLLI SKVFYFFFYS AYGSLYPLLP VYYKQLGMSP SQSGLLVGIR YFIEFCSAPF
WGVVADRFKK GKIVLLFSLL CWVLFNLGIG FVKPATLRCV PKIRPTTHPT NASHQLTILP
TNSSFTSFLT ISPKMREKRN LLETRLNVSD TVTLPTAPNM NSEPTLQPQT GEITNRMMDL
TLNSSTATPV SPGSVTKETT TVIVTTTKSL PSDQVMLVYD QQEVEAIFLV ILVVVIIGEF
FSASSVTIVD TVTLQYLGKH RDRYGLQRMW GSLGWGLAML SVGIGIDYTH IEVLIDGKGC
KPPEYRNYQI VFIVFGVLMT MALIVATQFR FRYNHFKNDD SKGKEVEIPQ VERNNSTESS
EETPTTTSHS QAFNFWDLIK LLCSVQYGSV LFVAWFMGFG YGFVFTFLYW HLEDLNGTTT
LFGVCSVLSH VSELTAYFFS HKLIELIGHI RVLYIGLACN TARYIYISYL ENAWTVLPME
VLQGVTHAAI WAACISYLSA AVPPELRTSA QGILQGLHLG LGRGCGAMIG GVLVNYFGAA
ATFRGIGMAC LVILLLFALI QWLAVPDEEE DKTMLAERIP VPSSPVPIAT IDLVQQQTED
VMPRIEPRLP PKKTKHQEEQ EDVNKPAWGV SSSPWVTFVY ALYQIKEMMQ LTRDNRASEI
QPLQGTNENR ENSPAGRAQP VPCETHSDPS RNQPSPDAAA SQTQTSPAHP SVDPCTEESE
EQQAQLAAGG H*

mutated AA sequence

MADDKVAILT DDEEEQKRKY VLADPFNGIS REPEPPSNET PSSTETSAIP EEEIDWIEKH
CVKINNDLLI SKVFYFFFYS AYGSLYPLLP VYYKQLGMSP SQSGLLVGIR YFIEFCSAPF
WGVVADRFKK GKIVLLFSLL CWVLFNLGIG FVKPATLRCV PKIRPTTHPT NASHQLTILP
TNSSFTSFLT ISPKMREKRN LLETGLNVSD TVTLPTAPNM NSEPTLQPQT GEITNRMMDL
TLNSSTATPV SPGSVTKETT TVIVTTTKSL PSDQVMLVYD QQEVEAIFLV ILVVVIIGEF
FSASSVTIVD TVTLQYLGKH RDRYGLQRMW GSLGWGLAML SVGIGIDYTH IEVLIDGKGC
KPPEYRNYQI VFIVFGVLMT MALIVATQFR FRYNHFKNDD SKGKEVEIPQ VERNNSTESS
EETPTTTSHS QAFNFWDLIK LLCSVQYGSV LFVAWFMGFG YGFVFTFLYW HLEDLNGTTT
LFGVCSVLSH VSELTAYFFS HKLIELIGHI RVLYIGLACN TARYIYISYL ENAWTVLPME
VLQGVTHAAI WAACISYLSA AVPPELRTSA QGILQGLHLG LGRGCGAMIG GVLVNYFGAA
ATFRGIGMAC LVILLLFALI QWLAVPDEEE DKTMLAERIP VPSSPVPIAT IDLVQQQTED
VMPRIEPRLP PKKTKHQEEQ EDVNKPAWGV SSSPWVTFVY ALYQIKEMMQ LTRDNRASEI
QPLQGTNENR ENSPAGRAQP VPCETHSDPS RNQPSPDAAA SQTQTSPAHP SVDPCTEESE
EQQAQLAAGG H*

speed

0.73 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

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999576 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:191301368A>GN/A show variant in all transcripts IGV

HGNC symbol

MFSD6

Ensembl transcript ID

ENST00000281416

Genbank transcript ID

N/A

UniProt peptide

Q6ZSS7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.613A>G
cDNA.748A>G
g.28288A>G

AA changes

R205G Score: 125 explain score(s)

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

205

frameshift

known variant

Reference ID: rs9646748

database	homozygous (G/G)	heterozygous	allele carriers
1000G	659	1148	1807
ExAC	15029	2709	17738

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.563	0
	2.072	0.006
(flanking)	-0.458	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

748

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

205

mutated

not conserved

205

Ptroglodytes

not conserved

ENSPTRG00000012743

205

Mmulatta

not conserved

ENSMMUG00000007289

205

Fcatus

not conserved

ENSFCAG00000005191

201

Mmusculus

not conserved

ENSMUSG00000041439

206

DVQ

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000032318

207

IGQYPWRTILSSGQSSGYIS

Dmelanogaster

not conserved

FBgn0033958

232

Celegans

not conserved

R13A5.9

154

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2376 / 2376

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

792 / 792

position of stopcodon in wt / mu cDNA

2511 / 2511

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

136 / 136

chromosome

strand

last intron/exon boundary

2308

theoretical NMD boundary in CDS

2122

length of CDS

2376

coding sequence (CDS) position

613

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

748

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

28288

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

191301368

original gDNA sequence snippet

AAAGAAACCTTTTGGAAACAAGGCTCAATGTCTCAGACACC

altered gDNA sequence snippet

AAAGAAACCTTTTGGAAACAGGGCTCAATGTCTCAGACACC

original cDNA sequence snippet

AAAGAAACCTTTTGGAAACAAGGCTCAATGTCTCAGACACC

altered cDNA sequence snippet

AAAGAAACCTTTTGGAAACAGGGCTCAATGTCTCAGACACC

wildtype AA sequence

mutated AA sequence

MADDKVAILT DDEEEQKRKY VLADPFNGIS REPEPPSNET PSSTETSAIP EEEIDWIEKH
CVKINNDLLI SKVFYFFFYS AYGSLYPLLP VYYKQLGMSP SQSGLLVGIR YFIEFCSAPF
WGVVADRFKK GKIVLLFSLL CWVLFNLGIG FVKPATLRCV PKIRPTTHPT NASHQLTILP
TNSSFTSFLT ISPKMREKRN LLETGLNVSD TVTLPTAPNM NSEPTLQPQT GEITNRMMDL
TLNSSTATPV SPGSVTKETT TVIVTTTKSL PSDQVMLVYD QQEVEAIFLV ILVVVIIGEF
FSASSVTIVD TVTLQYLGKH RDRYGLQRMW GSLGWGLAML SVGIGIDYTH IEVLIDGKGC
KPPEYRNYQI VFIVFGVLMT MALIVATQFR FRYNHFKNDD SKGKEVEIPQ VERNNSTESS
EETPTTTSHS QAFNFWDLIK LLCSVQYGSV LFVAWFMGFG YGFVFTFLYW HLEDLNGTTT
LFGVCSVLSH VSELTAYFFS HKLIELIGHI RVLYIGLACN TARYIYISYL ENAWTVLPME
VLQGVTHAAI WAACISYLSA AVPPELRTSA QGILQGLHLG LGRGCGAMIG GVLVNYFGAA
ATFRGIGMAC LVILLLFALI QWLAVPDEEE DKTMLAERIP VPSSPVPIAT IDLVQQQTED
VMPRIEPRLP PKKTKHQEEQ EDVNKPAWGV SSSPWVTFVY ALYQIKEMMQ LTRDNRASEI
QPLQGTNENR ENSPAGRAQP VPCETHSDPS RNQPSPDAAA SQTQTSPAHP SVDPCTEESE
EQQAQLAAGG H*

speed

0.37 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems