MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000460742
Querying Taster for transcript #2: ENST00000503680
Querying Taster for transcript #3: ENST00000379586
Querying Taster for transcript #4: ENST00000426700
Querying Taster for transcript #5: ENST00000259983
MT speed 0 s - this script 5.381652 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C6orf52	polymorphism_automatic	1.28197452653467e-12	simple_aae				A13D	single base exchange	rs7749306		show file
C6orf52	polymorphism_automatic	1.28197452653467e-12	simple_aae				A13D	single base exchange	rs7749306		show file
C6orf52	polymorphism_automatic	1.08123913045155e-07	without_aae					single base exchange	rs7749306		show file
C6orf52	polymorphism_automatic	1.08123913045155e-07	without_aae					single base exchange	rs7749306		show file
C6orf52	polymorphism_automatic	1.08123913045155e-07	without_aae					single base exchange	rs7749306		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998718 (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)

chr6:10687746G>TN/A show variant in all transcripts IGV

HGNC symbol

C6orf52

Ensembl transcript ID

ENST00000426700

Genbank transcript ID

N/A

UniProt peptide

Q5T4I8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.38C>A
cDNA.38C>A
g.7285C>A

AA changes

A13D Score: 126 explain score(s)

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

frameshift

known variant

Reference ID: rs7749306

database	homozygous (T/T)	heterozygous	allele carriers
1000G	412	391	803
ExAC	556	1290	1846

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.007	0.001
	0.387	0.001
(flanking)	-0.345	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
Donor marginally increased	7288	wt: 0.9826 / mu: 0.9839 (marginal change - not scored)	wt: AGCTCAACAAAATAA mu: AGATCAACAAAATAA	CTCA\|acaa

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

ENSPTRG00000017718

Mmulatta

no alignment

ENSMMUG00000018786

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no alignment

ENSGALG00000001310

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000036015

n/a

Dmelanogaster

not conserved

FBgn0031607

190

Celegans

no alignment

T07F10.3

n/a

Xtropicalis

no alignment

ENSXETG00000014263

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

459 / 459

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

153 / 153

position of stopcodon in wt / mu cDNA

459 / 459

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

317

theoretical NMD boundary in CDS

266

length of CDS

459

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)

7285

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

10687746

original gDNA sequence snippet

TTCTGCAGATTTTGGCATAGCTCAACAAAATAACTATTACT

altered gDNA sequence snippet

TTCTGCAGATTTTGGCATAGATCAACAAAATAACTATTACT

original cDNA sequence snippet

TTCTGCAGATTTTGGCATAGCTCAACAAAATAACTATTACT

altered cDNA sequence snippet

TTCTGCAGATTTTGGCATAGATCAACAAAATAACTATTACT

wildtype AA sequence

MAQPESSADF GIAQQNNYYC YWQSLPSAIR VKQEFQPSQS YRYGNWYARQ HGSYLLSGYS
YGCAVDGNGK DCFSAHETPE HTAGTLVMPK ETTPLAENQD EDPLEDPHLH LNIEESNQEF
MVKSEELYDS LMNCHWQPLD TVHSEIPDET PK*

mutated AA sequence

MAQPESSADF GIDQQNNYYC YWQSLPSAIR VKQEFQPSQS YRYGNWYARQ HGSYLLSGYS
YGCAVDGNGK DCFSAHETPE HTAGTLVMPK ETTPLAENQD EDPLEDPHLH LNIEESNQEF
MVKSEELYDS LMNCHWQPLD TVHSEIPDET PK*

speed

0.45 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: 0.999999999998718 (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)

chr6:10687746G>TN/A show variant in all transcripts IGV

HGNC symbol

C6orf52

Ensembl transcript ID

ENST00000259983

Genbank transcript ID

NM_001145020

UniProt peptide

Q5T4I8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.38C>A
cDNA.162C>A
g.7285C>A

AA changes

A13D Score: 126 explain score(s)

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

frameshift

known variant

Reference ID: rs7749306

database	homozygous (T/T)	heterozygous	allele carriers
1000G	412	391	803
ExAC	556	1290	1846

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.007	0.001
	0.387	0.001
(flanking)	-0.345	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
Donor marginally increased	7288	wt: 0.9826 / mu: 0.9839 (marginal change - not scored)	wt: AGCTCAACAAAATAA mu: AGATCAACAAAATAA	CTCA\|acaa

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

ENSPTRG00000017718

Mmulatta

no alignment

ENSMMUG00000018786

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no alignment

ENSGALG00000001310

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000036015

n/a

Dmelanogaster

not conserved

FBgn0031607

190

Celegans

no alignment

T07F10.3

n/a

Xtropicalis

no alignment

ENSXETG00000014263

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

459 / 459

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

153 / 153

position of stopcodon in wt / mu cDNA

583 / 583

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

125 / 125

chromosome

strand

-1

last intron/exon boundary

441

theoretical NMD boundary in CDS

266

length of CDS

459

coding sequence (CDS) position

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

162

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

7285

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

10687746

original gDNA sequence snippet

TTCTGCAGATTTTGGCATAGCTCAACAAAATAACTATTACT

altered gDNA sequence snippet

TTCTGCAGATTTTGGCATAGATCAACAAAATAACTATTACT

original cDNA sequence snippet

TTCTGCAGATTTTGGCATAGCTCAACAAAATAACTATTACT

altered cDNA sequence snippet

TTCTGCAGATTTTGGCATAGATCAACAAAATAACTATTACT

wildtype AA sequence

MAQPESSADF GIAQQNNYYC YWQSLPSAIR VKQEFQPSQS YRYGNWYARQ HGSYLLSGYS
YGCAVDGNGK DCFSAHETPE HTAGTLVMPK ETTPLAENQD EDPLEDPHLH LNIEESNQEF
MVKSEELYDS LMNCHWQPLD TVHSEIPDET PK*

mutated AA sequence

MAQPESSADF GIDQQNNYYC YWQSLPSAIR VKQEFQPSQS YRYGNWYARQ HGSYLLSGYS
YGCAVDGNGK DCFSAHETPE HTAGTLVMPK ETTPLAENQD EDPLEDPHLH LNIEESNQEF
MVKSEELYDS LMNCHWQPLD TVHSEIPDET PK*

speed

1.35 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999891876087 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:10687746G>TN/A show variant in all transcripts IGV

HGNC symbol

C6orf52

Ensembl transcript ID

ENST00000460742

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.7285C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7749306

database	homozygous (T/T)	heterozygous	allele carriers
1000G	412	391	803
ExAC	556	1290	1846

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.007	0.001
	0.387	0.001
(flanking)	-0.345	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
Donor marginally increased	7288	wt: 0.9826 / mu: 0.9839 (marginal change - not scored)	wt: AGCTCAACAAAATAA mu: AGATCAACAAAATAA	CTCA\|acaa

distance from splice site

349

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

312 / 312

chromosome

strand

-1

last intron/exon boundary

361

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

192

coding sequence (CDS) position

N/A

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

N/A

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

7285

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

10687746

original gDNA sequence snippet

TTCTGCAGATTTTGGCATAGCTCAACAAAATAACTATTACT

altered gDNA sequence snippet

TTCTGCAGATTTTGGCATAGATCAACAAAATAACTATTACT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

METTPLAENQ DEDPLEDPHL HLNIEESNQE FMVKSEELYD SLMNCHWQPL DTVHSEIPDE
TPK*

mutated AA sequence

N/A

speed

0.99 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999891876087 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:10687746G>TN/A show variant in all transcripts IGV

HGNC symbol

C6orf52

Ensembl transcript ID

ENST00000379586

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.7285C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7749306

database	homozygous (T/T)	heterozygous	allele carriers
1000G	412	391	803
ExAC	556	1290	1846

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.007	0.001
	0.387	0.001
(flanking)	-0.345	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
Donor marginally increased	7288	wt: 0.9826 / mu: 0.9839 (marginal change - not scored)	wt: AGCTCAACAAAATAA mu: AGATCAACAAAATAA	CTCA\|acaa

distance from splice site

457

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

199 / 199

chromosome

strand

-1

last intron/exon boundary

254

theoretical NMD boundary in CDS

length of CDS

198

coding sequence (CDS) position

N/A

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

N/A

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

7285

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

10687746

original gDNA sequence snippet

TTCTGCAGATTTTGGCATAGCTCAACAAAATAACTATTACT

altered gDNA sequence snippet

TTCTGCAGATTTTGGCATAGATCAACAAAATAACTATTACT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MPKETTPLAE NQDEDPLEDP HLHLNIEESN QEFMVKSEEL YDSLMNCHWQ PLDTVHSEIP
DETPK*

mutated AA sequence

N/A

speed

1.09 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999891876087 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:10687746G>TN/A show variant in all transcripts IGV

HGNC symbol

C6orf52

Ensembl transcript ID

ENST00000503680

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.7285C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7749306

database	homozygous (T/T)	heterozygous	allele carriers
1000G	412	391	803
ExAC	556	1290	1846

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.007	0.001
	0.387	0.001
(flanking)	-0.345	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
Donor marginally increased	7288	wt: 0.9826 / mu: 0.9839 (marginal change - not scored)	wt: AGCTCAACAAAATAA mu: AGATCAACAAAATAA	CTCA\|acaa

distance from splice site

349

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

367 / 367

chromosome

strand

-1

last intron/exon boundary

506

theoretical NMD boundary in CDS

length of CDS

282

coding sequence (CDS) position

N/A

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

N/A

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

7285

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

10687746

original gDNA sequence snippet

TTCTGCAGATTTTGGCATAGCTCAACAAAATAACTATTACT

altered gDNA sequence snippet

TTCTGCAGATTTTGGCATAGATCAACAAAATAACTATTACT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

METTPLAENQ DEDPLEVTSQ YVAQADLKLP DLSNSLVSAS QSVGVTDPHL HLNIEESNQE
FMVKSEELYD SLMNCHWQPL DTVHSEIPDE TPK*

mutated AA sequence

N/A

speed

1.01 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems