MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000395769
Querying Taster for transcript #2: ENST00000395771
Querying Taster for transcript #3: ENST00000319836
MT speed 0 s - this script 4.054286 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MARCHF8	polymorphism_automatic	0	simple_aae		affected		Y266H	single base exchange	rs7908745		show file
MARCHF8	polymorphism_automatic	0	simple_aae		affected		Y266H	single base exchange	rs7908745		show file
MARCHF8	polymorphism_automatic	0	simple_aae		affected		Y266H	single base exchange	rs7908745		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:45953767A>GN/A show variant in all transcripts IGV

HGNC symbol

MARCHF8

Ensembl transcript ID

ENST00000395769

Genbank transcript ID

NM_001002266

UniProt peptide

Q5T0T0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.796T>C
cDNA.1035T>C
g.136588T>C

AA changes

Y266H Score: 83 explain score(s)

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

266

frameshift

known variant

Reference ID: rs7908745

database	homozygous (G/G)	heterozygous	allele carriers
1000G	249	1019	1268
ExAC	6232	20303	26535

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.278	0.001
	0.459	0.001
(flanking)	-0.234	0.004

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	136579	wt: 0.48 / mu: 0.63	wt: AAAATAAACATGGAT mu: AAAATAAACATGGAC	AATA\|aaca
Donor marginally increased	136585	wt: 0.9211 / mu: 0.9754 (marginal change - not scored)	wt: AACATGGATATGGAA mu: AACATGGACATGGAA	CATG\|gata

distance from splice site

225

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

266

mutated

all conserved

266

Ptroglodytes

all conserved

ENSPTRG00000002459

430

Mmulatta

not conserved

ENSMMUG00000013437

430

Fcatus

not conserved

ENSFCAG00000013127

428

Mmusculus

all conserved

ENSMUSG00000025702

262

Ggallus

not conserved

ENSGALG00000005867

259

Trubripes

not conserved

ENSTRUG00000003760

490

Drerio

not conserved

ENSDARG00000062489

257

Dmelanogaster

no alignment

FBgn0035983

n/a

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000026961

460

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

876 / 876

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

292 / 292

position of stopcodon in wt / mu cDNA

1115 / 1115

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

240 / 240

chromosome

strand

-1

last intron/exon boundary

811

theoretical NMD boundary in CDS

521

length of CDS

876

coding sequence (CDS) position

796

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

1035

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

136588

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

45953767

original gDNA sequence snippet

ACTTTGAAAATAAACATGGATATGGAATCTGTCATTCCGAC

altered gDNA sequence snippet

ACTTTGAAAATAAACATGGACATGGAATCTGTCATTCCGAC

original cDNA sequence snippet

ACTTTGAAAATAAACATGGATATGGAATCTGTCATTCCGAC

altered cDNA sequence snippet

ACTTTGAAAATAAACATGGACATGGAATCTGTCATTCCGAC

wildtype AA sequence

MSMPLHQISA IPSQDAISAR VYRSKTKEKE REEQNEKTLG HFMSHSSNIS KAGSPPSASA
PAPVSSFSRT SITPSSQDIC RICHCEGDDE SPLITPCHCT GSLHFVHQAC LQQWIKSSDT
RCCELCKYEF IMETKLKPLR KWEKLQMTSS ERRKIMCSVT FHVIAITCVV WSLYVLIDRT
AEEIKQGQAT GILEWPFWTK LVVVAIGFTG GLLFMYVQCK VYVQLWKRLK AYNRVIYVQN
CPETSKKNIF EKSPLTEPNF ENKHGYGICH SDTNSSCCTE PEDTGAEIIH V*

mutated AA sequence

speed

1.17 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: 1 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:45953767A>GN/A show variant in all transcripts IGV

HGNC symbol

MARCHF8

Ensembl transcript ID

ENST00000395771

Genbank transcript ID

NM_001002265

UniProt peptide

Q5T0T0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.796T>C
cDNA.1639T>C
g.136588T>C

AA changes

Y266H Score: 83 explain score(s)

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

266

frameshift

known variant

Reference ID: rs7908745

database	homozygous (G/G)	heterozygous	allele carriers
1000G	249	1019	1268
ExAC	6232	20303	26535

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.278	0.001
	0.459	0.001
(flanking)	-0.234	0.004

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	136579	wt: 0.48 / mu: 0.63	wt: AAAATAAACATGGAT mu: AAAATAAACATGGAC	AATA\|aaca
Donor marginally increased	136585	wt: 0.9211 / mu: 0.9754 (marginal change - not scored)	wt: AACATGGATATGGAA mu: AACATGGACATGGAA	CATG\|gata

distance from splice site

225

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

266

mutated

all conserved

266

Ptroglodytes

all conserved

ENSPTRG00000002459

430

Mmulatta

not conserved

ENSMMUG00000013437

430

Fcatus

not conserved

ENSFCAG00000013127

428

Mmusculus

all conserved

ENSMUSG00000025702

262

Ggallus

not conserved

ENSGALG00000005867

259

Trubripes

not conserved

ENSTRUG00000003760

490

Drerio

not conserved

ENSDARG00000062489

257

Dmelanogaster

no alignment

FBgn0035983

n/a

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000026961

460

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

876 / 876

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

292 / 292

position of stopcodon in wt / mu cDNA

1719 / 1719

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

844 / 844

chromosome

strand

-1

last intron/exon boundary

1415

theoretical NMD boundary in CDS

521

length of CDS

876

coding sequence (CDS) position

796

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

1639

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

136588

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

45953767

original gDNA sequence snippet

ACTTTGAAAATAAACATGGATATGGAATCTGTCATTCCGAC

altered gDNA sequence snippet

ACTTTGAAAATAAACATGGACATGGAATCTGTCATTCCGAC

original cDNA sequence snippet

ACTTTGAAAATAAACATGGATATGGAATCTGTCATTCCGAC

altered cDNA sequence snippet

ACTTTGAAAATAAACATGGACATGGAATCTGTCATTCCGAC

wildtype AA sequence

mutated AA sequence

speed

1.16 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:45953767A>GN/A show variant in all transcripts IGV

HGNC symbol

MARCHF8

Ensembl transcript ID

ENST00000319836

Genbank transcript ID

NM_145021

UniProt peptide

Q5T0T0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.796T>C
cDNA.1546T>C
g.136588T>C

AA changes

Y266H Score: 83 explain score(s)

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

266

frameshift

known variant

Reference ID: rs7908745

database	homozygous (G/G)	heterozygous	allele carriers
1000G	249	1019	1268
ExAC	6232	20303	26535

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.278	0.001
	0.459	0.001
(flanking)	-0.234	0.004

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	136579	wt: 0.48 / mu: 0.63	wt: AAAATAAACATGGAT mu: AAAATAAACATGGAC	AATA\|aaca
Donor marginally increased	136585	wt: 0.9211 / mu: 0.9754 (marginal change - not scored)	wt: AACATGGATATGGAA mu: AACATGGACATGGAA	CATG\|gata

distance from splice site

225

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

266

mutated

all conserved

266

Ptroglodytes

all conserved

ENSPTRG00000002459

430

Mmulatta

not conserved

ENSMMUG00000013437

430

Fcatus

not conserved

ENSFCAG00000013127

428

Mmusculus

all conserved

ENSMUSG00000025702

262

Ggallus

not conserved

ENSGALG00000005867

259

Trubripes

not conserved

ENSTRUG00000003760

490

Drerio

not conserved

ENSDARG00000062489

257

Dmelanogaster

no alignment

FBgn0035983

n/a

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000026961

460

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

876 / 876

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

292 / 292

position of stopcodon in wt / mu cDNA

1626 / 1626

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

751 / 751

chromosome

strand

-1

last intron/exon boundary

1322

theoretical NMD boundary in CDS

521

length of CDS

876

coding sequence (CDS) position

796

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

1546

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

136588

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

45953767

original gDNA sequence snippet

ACTTTGAAAATAAACATGGATATGGAATCTGTCATTCCGAC

altered gDNA sequence snippet

ACTTTGAAAATAAACATGGACATGGAATCTGTCATTCCGAC

original cDNA sequence snippet

ACTTTGAAAATAAACATGGATATGGAATCTGTCATTCCGAC

altered cDNA sequence snippet

ACTTTGAAAATAAACATGGACATGGAATCTGTCATTCCGAC

wildtype AA sequence

mutated AA sequence

speed

0.49 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems