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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000310018
Querying Taster for transcript #2: ENST00000353492
Querying Taster for transcript #3: ENST00000393054
MT speed 0 s - this script 4.93269 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP6V0A4	disease_causing	0.99999999999782	simple_aae		affected		P524L	single base exchange	rs121908368		show file
ATP6V0A4	disease_causing	0.99999999999782	simple_aae		affected		P524L	single base exchange	rs121908368		show file
ATP6V0A4	disease_causing	0.99999999999782	simple_aae		affected		P524L	single base exchange	rs121908368		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999999782 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002226)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:138424286G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP6V0A4

Ensembl transcript ID

ENST00000310018

Genbank transcript ID

NM_020632

UniProt peptide

Q9HBG4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1571C>T
cDNA.1854C>T
g.60020C>T

AA changes

P524L Score: 98 explain score(s)

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

524

frameshift

known variant

Reference ID: rs121908368

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation at this position, please check HGMD for details (HGMD ID CM002226)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002226)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002226)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.378	1
	5.546	1
(flanking)	5.546	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	60021	sequence motif lost	-	wt: TCCG\|gtaa mu: TCTG.gtaa
Acc marginally increased	60011	wt: 0.2581 / mu: 0.3243 (marginal change - not scored)	wt: TGGAAATCCATACCCGTTTGGGATTGATCCGGTAATAATGT mu: TGGAAATCCATACCCGTTTGGGATTGATCTGGTAATAATGT	ttgg\|GATT
Donor lost	60021	0.23	wt: GATCCGGTAATAATG	TCCG\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

524

mutated

not conserved

524

Ptroglodytes

all identical

ENSPTRG00000019746

524

Mmulatta

all identical

ENSMMUG00000006547

524

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038600

524

Ggallus

all identical

ENSGALG00000012810

525

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0028671

538

Celegans

all identical

ZK637.8

557

Xtropicalis

all identical

ENSXETG00000011571

518

protein features

start (aa)	end (aa)	feature	details
474	538	TOPO_DOM	Vacuolar (Potential).	lost
539	558	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
559	576	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
577	597	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
598	642	TOPO_DOM	Vacuolar (Potential).	might get lost (downstream of altered splice site)
643	662	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
663	727	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
728	752	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
753	773	TOPO_DOM	Vacuolar (Potential).	might get lost (downstream of altered splice site)
774	812	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
813	840	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2523 / 2523

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

841 / 841

position of stopcodon in wt / mu cDNA

2806 / 2806

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

284 / 284

chromosome

strand

-1

last intron/exon boundary

2713

theoretical NMD boundary in CDS

2379

length of CDS

2523

coding sequence (CDS) position

1571

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

1854

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

60020

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

138424286

original gDNA sequence snippet

ATACCCGTTTGGGATTGATCCGGTAATAATGTCTTCTTGGG

altered gDNA sequence snippet

ATACCCGTTTGGGATTGATCTGGTAATAATGTCTTCTTGGG

original cDNA sequence snippet

ATACCCGTTTGGGATTGATCCGATTTGGAACTTGGCTTCAA

altered cDNA sequence snippet

ATACCCGTTTGGGATTGATCTGATTTGGAACTTGGCTTCAA

wildtype AA sequence

MVSVFRSEEM CLSQLFLQVE AAYCCVAELG ELGLVQFKDL NMNVNSFQRK FVNEVRRCES
LERILRFLED EMQNEIVVQL LEKSPLTPLP REMITLETVL EKLEGELQEA NQNQQALKQS
FLELTELKYL LKKTQDFFET ETNLADDFFT EDTSGLLELK AVPAYMTGKL GFIAGVINRE
RMASFERLLW RICRGNVYLK FSEMDAPLED PVTKEEIQKN IFIIFYQGEQ LRQKIKKICD
GFRATVYPCP EPAVERREML ESVNVRLEDL ITVITQTESH RQRLLQEAAA NWHSWLIKVQ
KMKAVYHILN MCNIDVTQQC VIAEIWFPVA DATRIKRALE QGMELSGSSM APIMTTVQSK
TAPPTFNRTN KFTAGFQNIV DAYGVGSYRE INPAPYTIIT FPFLFAVMFG DCGHGTVMLL
AALWMILNER RLLSQKTDNE IWNTFFHGRY LILLMGIFSI YTGLIYNDCF SKSLNIFGSS
WSVQPMFRNG TWNTHVMEES LYLQLDPAIP GVYFGNPYPF GIDPIWNLAS NKLTFLNSYK
MKMSVILGIV QMVFGVILSL FNHIYFRRTL NIILQFIPEM IFILCLFGYL VFMIIFKWCC
FDVHVSQHAP SILIHFINMF LFNYSDSSNA PLYKHQQEVQ SFFVVMALIS VPWMLLIKPF
ILRASHRKSQ LQASRIQEDA TENIEGDSSS PSSRSGQRTS ADTHGALDDH GEEFNFGDVF
VHQAIHTIEY CLGCISNTAS YLRLWALSLA HAQLSEVLWT MVMNSGLQTR GWGGIVGVFI
IFAVFAVLTV AILLIMEGLS AFLHALRLHW VEFQNKFYVG DGYKFSPFSF KHILDGTAEE
*

mutated AA sequence

MVSVFRSEEM CLSQLFLQVE AAYCCVAELG ELGLVQFKDL NMNVNSFQRK FVNEVRRCES
LERILRFLED EMQNEIVVQL LEKSPLTPLP REMITLETVL EKLEGELQEA NQNQQALKQS
FLELTELKYL LKKTQDFFET ETNLADDFFT EDTSGLLELK AVPAYMTGKL GFIAGVINRE
RMASFERLLW RICRGNVYLK FSEMDAPLED PVTKEEIQKN IFIIFYQGEQ LRQKIKKICD
GFRATVYPCP EPAVERREML ESVNVRLEDL ITVITQTESH RQRLLQEAAA NWHSWLIKVQ
KMKAVYHILN MCNIDVTQQC VIAEIWFPVA DATRIKRALE QGMELSGSSM APIMTTVQSK
TAPPTFNRTN KFTAGFQNIV DAYGVGSYRE INPAPYTIIT FPFLFAVMFG DCGHGTVMLL
AALWMILNER RLLSQKTDNE IWNTFFHGRY LILLMGIFSI YTGLIYNDCF SKSLNIFGSS
WSVQPMFRNG TWNTHVMEES LYLQLDPAIP GVYFGNPYPF GIDLIWNLAS NKLTFLNSYK
MKMSVILGIV QMVFGVILSL FNHIYFRRTL NIILQFIPEM IFILCLFGYL VFMIIFKWCC
FDVHVSQHAP SILIHFINMF LFNYSDSSNA PLYKHQQEVQ SFFVVMALIS VPWMLLIKPF
ILRASHRKSQ LQASRIQEDA TENIEGDSSS PSSRSGQRTS ADTHGALDDH GEEFNFGDVF
VHQAIHTIEY CLGCISNTAS YLRLWALSLA HAQLSEVLWT MVMNSGLQTR GWGGIVGVFI
IFAVFAVLTV AILLIMEGLS AFLHALRLHW VEFQNKFYVG DGYKFSPFSF KHILDGTAEE
*

speed

1.50 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

disease causing

Model: simple_aae, prob: 0.99999999999782 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002226)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:138424286G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP6V0A4

Ensembl transcript ID

ENST00000353492

Genbank transcript ID

N/A

UniProt peptide

Q9HBG4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1571C>T
cDNA.1659C>T
g.60020C>T

AA changes

P524L Score: 98 explain score(s)

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

524

frameshift

known variant

Reference ID: rs121908368

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.378	1
	5.546	1
(flanking)	5.546	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	60021	sequence motif lost	-	wt: TCCG\|gtaa mu: TCTG.gtaa
Acc marginally increased	60011	wt: 0.2581 / mu: 0.3243 (marginal change - not scored)	wt: TGGAAATCCATACCCGTTTGGGATTGATCCGGTAATAATGT mu: TGGAAATCCATACCCGTTTGGGATTGATCTGGTAATAATGT	ttgg\|GATT
Donor lost	60021	0.23	wt: GATCCGGTAATAATG	TCCG\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

524

mutated

not conserved

524

Ptroglodytes

all identical

ENSPTRG00000019746

524

Mmulatta

all identical

ENSMMUG00000006547

524

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038600

524

Ggallus

all identical

ENSGALG00000012810

525

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0028671

538

Celegans

all identical

ZK637.8

557

Xtropicalis

all identical

ENSXETG00000011571

518

protein features

start (aa)	end (aa)	feature	details
474	538	TOPO_DOM	Vacuolar (Potential).	lost
539	558	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
559	576	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
577	597	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
598	642	TOPO_DOM	Vacuolar (Potential).	might get lost (downstream of altered splice site)
643	662	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
663	727	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
728	752	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
753	773	TOPO_DOM	Vacuolar (Potential).	might get lost (downstream of altered splice site)
774	812	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
813	840	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2523 / 2523

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

841 / 841

position of stopcodon in wt / mu cDNA

2611 / 2611

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

89 / 89

chromosome

strand

-1

last intron/exon boundary

2518

theoretical NMD boundary in CDS

2379

length of CDS

2523

coding sequence (CDS) position

1571

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

1659

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

60020

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

138424286

original gDNA sequence snippet

ATACCCGTTTGGGATTGATCCGGTAATAATGTCTTCTTGGG

altered gDNA sequence snippet

ATACCCGTTTGGGATTGATCTGGTAATAATGTCTTCTTGGG

original cDNA sequence snippet

ATACCCGTTTGGGATTGATCCGATTTGGAACTTGGCTTCAA

altered cDNA sequence snippet

ATACCCGTTTGGGATTGATCTGATTTGGAACTTGGCTTCAA

wildtype AA sequence

mutated AA sequence

MVSVFRSEEM CLSQLFLQVE AAYCCVAELG ELGLVQFKDL NMNVNSFQRK FVNEVRRCES
LERILRFLED EMQNEIVVQL LEKSPLTPLP REMITLETVL EKLEGELQEA NQNQQALKQS
FLELTELKYL LKKTQDFFET ETNLADDFFT EDTSGLLELK AVPAYMTGKL GFIAGVINRE
RMASFERLLW RICRGNVYLK FSEMDAPLED PVTKEEIQKN IFIIFYQGEQ LRQKIKKICD
GFRATVYPCP EPAVERREML ESVNVRLEDL ITVITQTESH RQRLLQEAAA NWHSWLIKVQ
KMKAVYHILN MCNIDVTQQC VIAEIWFPVA DATRIKRALE QGMELSGSSM APIMTTVQSK
TAPPTFNRTN KFTAGFQNIV DAYGVGSYRE INPAPYTIIT FPFLFAVMFG DCGHGTVMLL
AALWMILNER RLLSQKTDNE IWNTFFHGRY LILLMGIFSI YTGLIYNDCF SKSLNIFGSS
WSVQPMFRNG TWNTHVMEES LYLQLDPAIP GVYFGNPYPF GIDLIWNLAS NKLTFLNSYK
MKMSVILGIV QMVFGVILSL FNHIYFRRTL NIILQFIPEM IFILCLFGYL VFMIIFKWCC
FDVHVSQHAP SILIHFINMF LFNYSDSSNA PLYKHQQEVQ SFFVVMALIS VPWMLLIKPF
ILRASHRKSQ LQASRIQEDA TENIEGDSSS PSSRSGQRTS ADTHGALDDH GEEFNFGDVF
VHQAIHTIEY CLGCISNTAS YLRLWALSLA HAQLSEVLWT MVMNSGLQTR GWGGIVGVFI
IFAVFAVLTV AILLIMEGLS AFLHALRLHW VEFQNKFYVG DGYKFSPFSF KHILDGTAEE
*

speed

1.30 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999999782 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002226)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:138424286G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP6V0A4

Ensembl transcript ID

ENST00000393054

Genbank transcript ID

NM_130841

UniProt peptide

Q9HBG4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1571C>T
cDNA.1809C>T
g.60020C>T

AA changes

P524L Score: 98 explain score(s)

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

524

frameshift

known variant

Reference ID: rs121908368

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.378	1
	5.546	1
(flanking)	5.546	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	60021	sequence motif lost	-	wt: TCCG\|gtaa mu: TCTG.gtaa
Acc marginally increased	60011	wt: 0.2581 / mu: 0.3243 (marginal change - not scored)	wt: TGGAAATCCATACCCGTTTGGGATTGATCCGGTAATAATGT mu: TGGAAATCCATACCCGTTTGGGATTGATCTGGTAATAATGT	ttgg\|GATT
Donor lost	60021	0.23	wt: GATCCGGTAATAATG	TCCG\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

524

mutated

not conserved

524

Ptroglodytes

all identical

ENSPTRG00000019746

524

Mmulatta

all identical

ENSMMUG00000006547

524

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038600

524

Ggallus

all identical

ENSGALG00000012810

525

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0028671

538

Celegans

all identical

ZK637.8

557

Xtropicalis

all identical

ENSXETG00000011571

518

protein features

start (aa)	end (aa)	feature	details
474	538	TOPO_DOM	Vacuolar (Potential).	lost
539	558	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
559	576	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
577	597	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
598	642	TOPO_DOM	Vacuolar (Potential).	might get lost (downstream of altered splice site)
643	662	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
663	727	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
728	752	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
753	773	TOPO_DOM	Vacuolar (Potential).	might get lost (downstream of altered splice site)
774	812	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
813	840	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2523 / 2523

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

841 / 841

position of stopcodon in wt / mu cDNA

2761 / 2761

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

239 / 239

chromosome

strand

-1

last intron/exon boundary

2668

theoretical NMD boundary in CDS

2379

length of CDS

2523

coding sequence (CDS) position

1571

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

1809

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

60020

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

138424286

original gDNA sequence snippet

ATACCCGTTTGGGATTGATCCGGTAATAATGTCTTCTTGGG

altered gDNA sequence snippet

ATACCCGTTTGGGATTGATCTGGTAATAATGTCTTCTTGGG

original cDNA sequence snippet

ATACCCGTTTGGGATTGATCCGATTTGGAACTTGGCTTCAA

altered cDNA sequence snippet

ATACCCGTTTGGGATTGATCTGATTTGGAACTTGGCTTCAA

wildtype AA sequence

mutated AA sequence

MVSVFRSEEM CLSQLFLQVE AAYCCVAELG ELGLVQFKDL NMNVNSFQRK FVNEVRRCES
LERILRFLED EMQNEIVVQL LEKSPLTPLP REMITLETVL EKLEGELQEA NQNQQALKQS
FLELTELKYL LKKTQDFFET ETNLADDFFT EDTSGLLELK AVPAYMTGKL GFIAGVINRE
RMASFERLLW RICRGNVYLK FSEMDAPLED PVTKEEIQKN IFIIFYQGEQ LRQKIKKICD
GFRATVYPCP EPAVERREML ESVNVRLEDL ITVITQTESH RQRLLQEAAA NWHSWLIKVQ
KMKAVYHILN MCNIDVTQQC VIAEIWFPVA DATRIKRALE QGMELSGSSM APIMTTVQSK
TAPPTFNRTN KFTAGFQNIV DAYGVGSYRE INPAPYTIIT FPFLFAVMFG DCGHGTVMLL
AALWMILNER RLLSQKTDNE IWNTFFHGRY LILLMGIFSI YTGLIYNDCF SKSLNIFGSS
WSVQPMFRNG TWNTHVMEES LYLQLDPAIP GVYFGNPYPF GIDLIWNLAS NKLTFLNSYK
MKMSVILGIV QMVFGVILSL FNHIYFRRTL NIILQFIPEM IFILCLFGYL VFMIIFKWCC
FDVHVSQHAP SILIHFINMF LFNYSDSSNA PLYKHQQEVQ SFFVVMALIS VPWMLLIKPF
ILRASHRKSQ LQASRIQEDA TENIEGDSSS PSSRSGQRTS ADTHGALDDH GEEFNFGDVF
VHQAIHTIEY CLGCISNTAS YLRLWALSLA HAQLSEVLWT MVMNSGLQTR GWGGIVGVFI
IFAVFAVLTV AILLIMEGLS AFLHALRLHW VEFQNKFYVG DGYKFSPFSF KHILDGTAEE
*

speed

1.37 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems