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: ENST00000505642
Querying Taster for transcript #2: ENST00000313303
MT speed 0 s - this script 2.73299 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C5orf64	polymorphism_automatic	2.99760216648792e-14	simple_aae				A57T	single base exchange	rs16893687		show file
C5orf64	polymorphism_automatic	2.99760216648792e-14	simple_aae				A57T	single base exchange	rs16893687		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999997 (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)

chr5:60982841G>AN/A show variant in all transcripts IGV

HGNC symbol

C5orf64

Ensembl transcript ID

ENST00000313303

Genbank transcript ID

N/A

UniProt peptide

Q2M2E5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.169G>A
cDNA.198G>A
g.49307G>A

AA changes

A57T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs16893687

database	homozygous (A/A)	heterozygous	allele carriers
1000G	651	1180	1831
ExAC	11893	8981	20874

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.027	0.008
	-0.215	0.001
(flanking)	0.309	0.002

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	49307	wt: 0.9939 / mu: 0.9970 (marginal change - not scored)	wt: TGACCGCTGAAGTTT mu: TGACCACTGAAGTTT	ACCG\|ctga

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

not conserved

ENSPTRG00000016911

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

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

393 / 393

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

131 / 131

position of stopcodon in wt / mu cDNA

422 / 422

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

30 / 30

chromosome

strand

last intron/exon boundary

255

theoretical NMD boundary in CDS

175

length of CDS

393

coding sequence (CDS) position

169

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

198

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

49307

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

60982841

original gDNA sequence snippet

CACCACCCAAGGATCTGACCGCTGAAGTTTACTTCCCTTCA

altered gDNA sequence snippet

CACCACCCAAGGATCTGACCACTGAAGTTTACTTCCCTTCA

original cDNA sequence snippet

CACCACCCAAGGATCTGACCGCTGAAGTTTACTTCCCTTCA

altered cDNA sequence snippet

CACCACCCAAGGATCTGACCACTGAAGTTTACTTCCCTTCA

wildtype AA sequence

MLAPLFLCCL RNLFRKLISF QPPQLGRTNM HYSKLPRTAI ETEFKQNVGP PPKDLTAEVY
FPSIKSRSHL PAVFYNQYFK HPKCVGEYGP KNGAERQIEE RKVLPTTMMF SMLADCVLKS
TPIPILGVAM *

mutated AA sequence

MLAPLFLCCL RNLFRKLISF QPPQLGRTNM HYSKLPRTAI ETEFKQNVGP PPKDLTTEVY
FPSIKSRSHL PAVFYNQYFK HPKCVGEYGP KNGAERQIEE RKVLPTTMMF SMLADCVLKS
TPIPILGVAM *

speed

0.35 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: 0.99999999999997 (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)

chr5:60982841G>AN/A show variant in all transcripts IGV

HGNC symbol

C5orf64

Ensembl transcript ID

ENST00000505642

Genbank transcript ID

NM_173667

UniProt peptide

Q2M2E5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.169G>A
cDNA.244G>A
g.49307G>A

AA changes

A57T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs16893687

database	homozygous (A/A)	heterozygous	allele carriers
1000G	651	1180	1831
ExAC	11893	8981	20874

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.027	0.008
	-0.215	0.001
(flanking)	0.309	0.002

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	49307	wt: 0.9939 / mu: 0.9970 (marginal change - not scored)	wt: TGACCGCTGAAGTTT mu: TGACCACTGAAGTTT	ACCG\|ctga

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

not conserved

ENSPTRG00000016911

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

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

393 / 393

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

131 / 131

position of stopcodon in wt / mu cDNA

468 / 468

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

76 / 76

chromosome

strand

last intron/exon boundary

301

theoretical NMD boundary in CDS

175

length of CDS

393

coding sequence (CDS) position

169

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

244

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

49307

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

60982841

original gDNA sequence snippet

CACCACCCAAGGATCTGACCGCTGAAGTTTACTTCCCTTCA

altered gDNA sequence snippet

CACCACCCAAGGATCTGACCACTGAAGTTTACTTCCCTTCA

original cDNA sequence snippet

CACCACCCAAGGATCTGACCGCTGAAGTTTACTTCCCTTCA

altered cDNA sequence snippet

CACCACCCAAGGATCTGACCACTGAAGTTTACTTCCCTTCA

wildtype AA sequence

MLAPLFLCCL RNLFRKLISF QPPQLGRTNM HYSKLPRTAI ETEFKQNVGP PPKDLTAEVY
FPSIKSRSHL PAVFYNQYFK HPKCVGEYGP KNGAERQIEE RKVLPTTMMF SMLADCVLKS
TPIPILGVAM *

mutated AA sequence

MLAPLFLCCL RNLFRKLISF QPPQLGRTNM HYSKLPRTAI ETEFKQNVGP PPKDLTTEVY
FPSIKSRSHL PAVFYNQYFK HPKCVGEYGP KNGAERQIEE RKVLPTTMMF SMLADCVLKS
TPIPILGVAM *

speed

0.81 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems