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: ENST00000449250
Querying Taster for transcript #2: ENST00000536693
Querying Taster for transcript #3: ENST00000334461
MT speed 0 s - this script 4.209281 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C17orf58	polymorphism_automatic	6.79456491070596e-14	simple_aae		affected		I92V	single base exchange	rs9891146		show file
C17orf58	polymorphism_automatic	1.53368288957623e-07	without_aae		affected			single base exchange	rs9891146		show file
C17orf58	polymorphism_automatic	1.53368288957623e-07	without_aae		affected			single base exchange	rs9891146		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999932 (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)

chr17:65988049T>CN/A show variant in all transcripts IGV

HGNC symbol

C17orf58

Ensembl transcript ID

ENST00000449250

Genbank transcript ID

NM_181655

UniProt peptide

Q2M2W7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.274A>G
cDNA.464A>G
g.1717A>G

AA changes

I92V Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs9891146

database	homozygous (C/C)	heterozygous	allele carriers
1000G	693	1053	1746
ExAC	25842	-18917	6925

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.546	0.01
	-0.135	0.002
(flanking)	-0.473	0.007

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 gained	1711	0.93	mu: TTCAAGGTGCAGTTC	CAAG\|gtgc

distance from splice site

171

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

no alignment

ENSPTRG00000009569

n/a

Mmulatta

all identical

ENSMMUG00000003211

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000003590

Trubripes

not conserved

ENSTRUG00000002742

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

294 / 294

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

98 / 98

position of stopcodon in wt / mu cDNA

484 / 484

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

191 / 191

chromosome

strand

-1

last intron/exon boundary

294

theoretical NMD boundary in CDS

length of CDS

294

coding sequence (CDS) position

274

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

464

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

1717

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

65988049

original gDNA sequence snippet

AAGGGCAGATTCAAGGTGCAATTCATACCCAATGCATTTGA

altered gDNA sequence snippet

AAGGGCAGATTCAAGGTGCAGTTCATACCCAATGCATTTGA

original cDNA sequence snippet

AAGGGCAGATTCAAGGTGCAATTCATACCCAATGCATTTGA

altered cDNA sequence snippet

AAGGGCAGATTCAAGGTGCAGTTCATACCCAATGCATTTGA

wildtype AA sequence

MNRLYLTPDG FFFRVHMLAL DSSSCNKPCP EFKPGSRYIV MGHIYHKRRQ LPTALLQVLR
GRLRPGDGLL RSSSSYVKRF NRKREGQIQG AIHTQCI*

mutated AA sequence

MNRLYLTPDG FFFRVHMLAL DSSSCNKPCP EFKPGSRYIV MGHIYHKRRQ LPTALLQVLR
GRLRPGDGLL RSSSSYVKRF NRKREGQIQG AVHTQCI*

speed

1.02 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: without_aae, prob: 0.999999846631711 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:65988049T>CN/A show variant in all transcripts IGV

HGNC symbol

C17orf58

Ensembl transcript ID

ENST00000536693

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.823A>G
g.1717A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs9891146

database	homozygous (C/C)	heterozygous	allele carriers
1000G	693	1053	1746
ExAC	25842	-18917	6925

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.546	0.01
	-0.135	0.002
(flanking)	-0.473	0.007

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

splice sites

splice site change occurs after stopcodon (at aa 138)

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	1711	0.93	mu: TTCAAGGTGCAGTTC	CAAG\|gtgc

distance from splice site

171

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

407 / 407

chromosome

strand

-1

last intron/exon boundary

653

theoretical NMD boundary in CDS

196

length of CDS

228

coding sequence (CDS) position

N/A

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

823

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

1717

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

65988049

original gDNA sequence snippet

AAGGGCAGATTCAAGGTGCAATTCATACCCAATGCATTTGA

altered gDNA sequence snippet

AAGGGCAGATTCAAGGTGCAGTTCATACCCAATGCATTTGA

original cDNA sequence snippet

AAGGGCAGATTCAAGGTGCAATTCATACCCAATGCATTTGA

altered cDNA sequence snippet

AAGGGCAGATTCAAGGTGCAGTTCATACCCAATGCATTTGA

wildtype AA sequence

MNRLYLTPDG FFFRVHMLAL DSSSCNKPCP EFKPGIETDL NDAAYVLYTT VCNVGATARA
VGRPAFFWER WETMT*

mutated AA sequence

N/A

speed

1.22 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999846631711 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:65988049T>CN/A show variant in all transcripts IGV

HGNC symbol

C17orf58

Ensembl transcript ID

ENST00000334461

Genbank transcript ID

NM_181656

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.732A>G
g.1717A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs9891146

database	homozygous (C/C)	heterozygous	allele carriers
1000G	693	1053	1746
ExAC	25842	-18917	6925

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.546	0.01
	-0.135	0.002
(flanking)	-0.473	0.007

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

splice sites

splice site change occurs after stopcodon (at aa 138)

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	1711	0.93	mu: TTCAAGGTGCAGTTC	CAAG\|gtgc

distance from splice site

171

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

316 / 316

chromosome

strand

-1

last intron/exon boundary

562

theoretical NMD boundary in CDS

196

length of CDS

228

coding sequence (CDS) position

N/A

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

732

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

1717

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

65988049

original gDNA sequence snippet

AAGGGCAGATTCAAGGTGCAATTCATACCCAATGCATTTGA

altered gDNA sequence snippet

AAGGGCAGATTCAAGGTGCAGTTCATACCCAATGCATTTGA

original cDNA sequence snippet

AAGGGCAGATTCAAGGTGCAATTCATACCCAATGCATTTGA

altered cDNA sequence snippet

AAGGGCAGATTCAAGGTGCAGTTCATACCCAATGCATTTGA

wildtype AA sequence

MNRLYLTPDG FFFRVHMLAL DSSSCNKPCP EFKPGIETDL NDAAYVLYTT VCNVGATARA
VGRPAFFWER WETMT*

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

Problems