MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000359187
Querying Taster for transcript #2: ENST00000360553
Querying Taster for transcript #3: ENST00000432566
Querying Taster for transcript #4: ENST00000543376
MT speed 0 s - this script 3.982144 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GOLGA8A	polymorphism_automatic	2.91778450289826e-08	simple_aae		affected		V425I	single base exchange	rs347877		show file
GOLGA8A	polymorphism_automatic	8.37844039702773e-08	simple_aae		affected		V568I	single base exchange	rs347877		show file
GOLGA8A	polymorphism_automatic	8.37844039702773e-08	simple_aae		affected		V568I	single base exchange	rs347877		show file
GOLGA8A	polymorphism_automatic	1.87970485954203e-07	simple_aae		affected		V598I	single base exchange	rs347877		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999970822155 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:34673722C>TN/A show variant in all transcripts IGV

HGNC symbol

GOLGA8A

Ensembl transcript ID

ENST00000543376

Genbank transcript ID

N/A

UniProt peptide

A7E2F4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1273G>A
cDNA.4028G>A
g.206983G>A

AA changes

V425I Score: 29 explain score(s)

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

425

frameshift

known variant

Reference ID: rs347877

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	9217	14333	23550

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.691	1
	0.512	0.998
(flanking)	-0.349	0.996

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	206985	wt: 0.40 / mu: 0.87	wt: CCAGTCGTGCAGCTC mu: CCAATCGTGCAGCTC	AGTC\|gtgc
Donor marginally increased	206978	wt: 0.8832 / mu: 0.9436 (marginal change - not scored)	wt: TGCACAGCCAGTCGT mu: TGCACAGCCAATCGT	CACA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

425

mutated

all conserved

425

Ptroglodytes

all conserved

ENSPTRG00000030342

567

Mmulatta

all conserved

ENSMMUG00000014208

220

AQEH

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

all conserved

ENSGALG00000004881

964

Trubripes

all conserved

ENSTRUG00000018651

981

QGTAR

Drerio

no alignment

ENSDARG00000063197

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000012915

978

protein features

start (aa)	end (aa)	feature	details
110	468	COILED	Potential.	lost
519	631	REGION	Golgi-targeting domain (By similarity).	might get lost (downstream of altered splice site)
596	596	CONFLICT	V -> I (in Ref. 1; AAF28463, 2; BAA74878, 4; AAI44610/AAI50330/AAI52411 and 5; CAH18214).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1383 / 1383

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

461 / 461

position of stopcodon in wt / mu cDNA

4138 / 4138

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

2756 / 2756

chromosome

strand

-1

last intron/exon boundary

3936

theoretical NMD boundary in CDS

1130

length of CDS

1383

coding sequence (CDS) position

1273

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

4028

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

206983

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

34673722

original gDNA sequence snippet

ACAACCCTACTGCACAGCCAGTCGTGCAGCTCCTTGGTGAG

altered gDNA sequence snippet

ACAACCCTACTGCACAGCCAATCGTGCAGCTCCTTGGTGAG

original cDNA sequence snippet

ACAACCCTACTGCACAGCCAGTCGTGCAGCTCCTTGGTGAG

altered cDNA sequence snippet

ACAACCCTACTGCACAGCCAATCGTGCAGCTCCTTGGTGAG

wildtype AA sequence

MKHSLRYFEE ESKDLAGRLQ RSSQRIGELE WSLCAVAATQ KKKPDGFSSR SKALLKRQLE
QSIREQILLK GHVTQLKESL KEVQLERDQY AEQIKGERAQ WQQRMRKMSQ EVCTLKEEKK
HDTHRVEELE RSLSRLKNQM AEPLPPDAPA VSSEVELQDL RKELERVAGE LQAQVENNQC
ISLLNRGQKE RLREQEERLQ EQQERLRERE KRLQQLAEPQ SDLEELKHEN KSALQLEQQV
KELQEKLGQV METLTSAEKE PEAAVPASGT GGESSGLMDL LEEKADLREH VEKLELGFIQ
YRRERCHQKV HRLLTEPGDS AKDASPGGGH HQAGPGQGGE EGEAAGAAGD GVAACGSYSE
GHGKFLAAAR NPAAEPSPGA PAPQELGAAD KHGDLCEASL TNSVEPAQGE AREGSSQDNP
TAQPVVQLLG EMQDHQEHPG LGSNCCVPCF CWAWLPRRRR *

mutated AA sequence

speed

0.95 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: 0.999999916215596 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:34673722C>TN/A show variant in all transcripts IGV

HGNC symbol

GOLGA8A

Ensembl transcript ID

ENST00000359187

Genbank transcript ID

N/A

UniProt peptide

A7E2F4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1702G>A
cDNA.1767G>A
g.206983G>A

AA changes

V568I Score: 29 explain score(s)

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

568

frameshift

known variant

Reference ID: rs347877

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	9217	14333	23550

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.691	1
	0.512	0.998
(flanking)	-0.349	0.996

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	206985	wt: 0.40 / mu: 0.87	wt: CCAGTCGTGCAGCTC mu: CCAATCGTGCAGCTC	AGTC\|gtgc
Donor marginally increased	206978	wt: 0.8832 / mu: 0.9436 (marginal change - not scored)	wt: TGCACAGCCAGTCGT mu: TGCACAGCCAATCGT	CACA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

568

mutated

all conserved

568

Ptroglodytes

all conserved

ENSPTRG00000030342

567

Mmulatta

all conserved

ENSMMUG00000014208

220

AQEH

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no alignment

ENSGALG00000004881

n/a

Trubripes

no alignment

ENSTRUG00000018651

n/a

Drerio

no alignment

ENSDARG00000063197

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000012915

977

protein features

start (aa)	end (aa)	feature	details
519	631	REGION	Golgi-targeting domain (By similarity).	lost
596	596	CONFLICT	V -> I (in Ref. 1; AAF28463, 2; BAA74878, 4; AAI44610/AAI50330/AAI52411 and 5; CAH18214).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1812 / 1812

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

604 / 604

position of stopcodon in wt / mu cDNA

1877 / 1877

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

66 / 66

chromosome

strand

-1

last intron/exon boundary

1675

theoretical NMD boundary in CDS

1559

length of CDS

1812

coding sequence (CDS) position

1702

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

1767

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

206983

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

34673722

original gDNA sequence snippet

ACAACCCTACTGCACAGCCAGTCGTGCAGCTCCTTGGTGAG

altered gDNA sequence snippet

ACAACCCTACTGCACAGCCAATCGTGCAGCTCCTTGGTGAG

original cDNA sequence snippet

ACAACCCTACTGCACAGCCAGTCGTGCAGCTCCTTGGTGAG

altered cDNA sequence snippet

ACAACCCTACTGCACAGCCAATCGTGCAGCTCCTTGGTGAG

wildtype AA sequence

MAEETGQSKL AAAKKKFKEY WQRNRPGVPA AAKRNTKANG SSPETAASGG CHSSEASSSA
SSSLHARQSP CQEQAAVLNS RSIKISRLND TIKSLKQQKK QVEHQLEEEK KANNEKQKAE
RELEGQIQRL NTEKKKLNTD LYHMKHSLRY FEEESKDLAG RLQRSSQRIG ELEWSLCAVA
ATQKKKPDGF SSRSKALLKR QLEQSIREQI LLKGHVTQLK ESLKEVQLER DQYAEQIKGE
RAQWQQRMRK MSQEVCTLKE EKKHDTHRVE ELERSLSRLK NQMAEPLPPD APAVSSEVEL
QDLRKELERV AGELQAQVEN NQCISLLNRG QKERLREQEE RLQEQQERLR EREKRLQQLA
EPQSDLEELK HENKSALQLE QQVKELQEKL GQVMETLTSA EKEPEAAVPA SGTGGESSGL
MDLLEEKADL REHVEKLELG FIQYRRERCH QKVHRLLTEP GDSAKDASPG GGHHQAGPGQ
GGEEGEAAGA AGDGVAACGS YSEGHGKFLA AARNPAAEPS PGAPAPQELG AADKHGDLCE
ASLTNSVEPA QGEAREGSSQ DNPTAQPVVQ LLGEMQDHQE HPGLGSNCCV PCFCWAWLPR
RRR*

mutated AA sequence

speed

0.90 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999916215596 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:34673722C>TN/A show variant in all transcripts IGV

HGNC symbol

GOLGA8A

Ensembl transcript ID

ENST00000360553

Genbank transcript ID

NM_181077

UniProt peptide

A7E2F4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1702G>A
cDNA.2689G>A
g.206983G>A

AA changes

V568I Score: 29 explain score(s)

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

568

frameshift

known variant

Reference ID: rs347877

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	9217	14333	23550

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.691	1
	0.512	0.998
(flanking)	-0.349	0.996

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	206985	wt: 0.40 / mu: 0.87	wt: CCAGTCGTGCAGCTC mu: CCAATCGTGCAGCTC	AGTC\|gtgc
Donor marginally increased	206978	wt: 0.8832 / mu: 0.9436 (marginal change - not scored)	wt: TGCACAGCCAGTCGT mu: TGCACAGCCAATCGT	CACA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

568

mutated

all conserved

568

Ptroglodytes

all conserved

ENSPTRG00000030342

567

Mmulatta

all conserved

ENSMMUG00000014208

220

AQEH

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no alignment

ENSGALG00000004881

n/a

Trubripes

no alignment

ENSTRUG00000018651

n/a

Drerio

no alignment

ENSDARG00000063197

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000012915

977

protein features

start (aa)	end (aa)	feature	details
519	631	REGION	Golgi-targeting domain (By similarity).	lost
596	596	CONFLICT	V -> I (in Ref. 1; AAF28463, 2; BAA74878, 4; AAI44610/AAI50330/AAI52411 and 5; CAH18214).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1812 / 1812

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

604 / 604

position of stopcodon in wt / mu cDNA

2799 / 2799

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

988 / 988

chromosome

strand

-1

last intron/exon boundary

2597

theoretical NMD boundary in CDS

1559

length of CDS

1812

coding sequence (CDS) position

1702

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

2689

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

206983

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

34673722

original gDNA sequence snippet

ACAACCCTACTGCACAGCCAGTCGTGCAGCTCCTTGGTGAG

altered gDNA sequence snippet

ACAACCCTACTGCACAGCCAATCGTGCAGCTCCTTGGTGAG

original cDNA sequence snippet

ACAACCCTACTGCACAGCCAGTCGTGCAGCTCCTTGGTGAG

altered cDNA sequence snippet

ACAACCCTACTGCACAGCCAATCGTGCAGCTCCTTGGTGAG

wildtype AA sequence

mutated AA sequence

speed

0.88 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999812029514 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:34673722C>TN/A show variant in all transcripts IGV

HGNC symbol

GOLGA8A

Ensembl transcript ID

ENST00000432566

Genbank transcript ID

N/A

UniProt peptide

A7E2F4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1792G>A
cDNA.1792G>A
g.206983G>A

AA changes

V598I Score: 29 explain score(s)

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

598

frameshift

known variant

Reference ID: rs347877

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	9217	14333	23550

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.691	1
	0.512	0.998
(flanking)	-0.349	0.996

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	206985	wt: 0.40 / mu: 0.87	wt: CCAGTCGTGCAGCTC mu: CCAATCGTGCAGCTC	AGTC\|gtgc
Donor marginally increased	206978	wt: 0.8832 / mu: 0.9436 (marginal change - not scored)	wt: TGCACAGCCAGTCGT mu: TGCACAGCCAATCGT	CACA\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

598

mutated

all conserved

598

Ptroglodytes

all conserved

ENSPTRG00000030342

567

Mmulatta

all conserved

ENSMMUG00000014208

220

AQEH

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

all conserved

ENSGALG00000004881

963

Trubripes

all conserved

ENSTRUG00000018651

981

QGTAR

Drerio

all conserved

ENSDARG00000063197

1018

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000012915

979

protein features

start (aa)	end (aa)	feature	details
519	631	REGION	Golgi-targeting domain (By similarity).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1902 / 1902

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

634 / 634

position of stopcodon in wt / mu cDNA

1902 / 1902

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

1700

theoretical NMD boundary in CDS

1649

length of CDS

1902

coding sequence (CDS) position

1792

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

1792

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

206983

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

34673722

original gDNA sequence snippet

ACAACCCTACTGCACAGCCAGTCGTGCAGCTCCTTGGTGAG

altered gDNA sequence snippet

ACAACCCTACTGCACAGCCAATCGTGCAGCTCCTTGGTGAG

original cDNA sequence snippet

ACAACCCTACTGCACAGCCAGTCGTGCAGCTCCTTGGTGAG

altered cDNA sequence snippet

ACAACCCTACTGCACAGCCAATCGTGCAGCTCCTTGGTGAG

wildtype AA sequence

MLPVDGEERK SEGSDTEGDR TSPCAGPTSS ATLKDLEVGG SGRRCSDPAG QPSNLLPQRG
LGAPLPAETA HTQPSPNDRS LYLSPKSSSA SSSLHARQSP CQEQAAVLNS RSIKISRLND
TIKSLKQQKK QVEHQLEEEK KANNEKQKAE RELEGQIQRL NTEKKKLNTD LYHMKHSLRY
FEEESKDLAG RLQRSSQRIG ELEWSLCAVA ATQKKKPDGF SSRSKALLKR QLEQSIREQI
LLKGHVTQLK ESLKEVQLER DQYAEQIKGE RAQWQQRMRK MSQEVCTLKE EKKHDTHRVE
ELERSLSRLK NQMAEPLPPD APAVSSEVEL QDLRKELERV AGELQAQVEN NQCISLLNRG
QKERLREQEE RLQEQQERLR EREKRLQQLA EPQSDLEELK HENKSALQLE QQVKELQEKL
GQVMETLTSA EKEPEAAVPA SGTGGESSGL MDLLEEKADL REHVEKLELG FIQYRRERCH
QKVHRLLTEP GDSAKDASPG GGHHQAGPGQ GGEEGEAAGA AGDGVAACGS YSEGHGKFLA
AARNPAAEPS PGAPAPQELG AADKHGDLCE ASLTNSVEPA QGEAREGSSQ DNPTAQPVVQ
LLGEMQDHQE HPGLGSNCCV PCFCWAWLPR RRR*

mutated AA sequence

speed

0.64 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

Problems