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: ENST00000310018
Querying Taster for transcript #2: ENST00000353492
Querying Taster for transcript #3: ENST00000393054
MT speed 0 s - this script 4.303549 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP6V0A4	disease_causing_automatic	0.999740836456851	simple_aae		affected	0	R807Q	single base exchange	rs28939081		show file
ATP6V0A4	disease_causing_automatic	0.999740836456851	simple_aae		affected	0	R807Q	single base exchange	rs28939081		show file
ATP6V0A4	disease_causing_automatic	0.999740836456851	simple_aae		affected	0	R807Q	single base exchange	rs28939081		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999740836456851 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM023023)
known disease mutation: rs5159 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:138394378C>TN/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.2420G>A
cDNA.2703G>A
g.89928G>A

AA changes

R807Q Score: 43 explain score(s)

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

807

frameshift

known variant

Reference ID: rs28939081

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	2	2

known disease mutation: rs5159 (pathogenic for Renal tubular acidosis, distal, autosomal recessive) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM023023)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023023)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023023)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.334	0.016
	3.482	0.742
(flanking)	0.503	0.723

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
Acc marginally increased	89918	wt: 0.9741 / mu: 0.9784 (marginal change - not scored)	wt: AGGGCCTCTCTGCTTTCCTGCACGCCCTGCGACTGCACTGG mu: AGGGCCTCTCTGCTTTCCTGCACGCCCTGCAACTGCACTGG	ctgc\|ACGC
Donor gained	89924	0.30	mu: ACGCCCTGCAACTGC	GCCC\|tgca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

807

mutated

all conserved

807

Ptroglodytes

all identical

ENSPTRG00000019746

807

Mmulatta

all identical

ENSMMUG00000006547

806

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038600

800

Ggallus

all identical

ENSGALG00000012810

804

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0028671

819

Celegans

all identical

ZK637.8

868

Xtropicalis

all identical

ENSXETG00000011571

805

protein features

start (aa)	end (aa)	feature	details
774	812	TRANSMEM	Helical; (Potential).	lost
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

2420

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

2703

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

89928

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

138394378

original gDNA sequence snippet

TGCTTTCCTGCACGCCCTGCGACTGCACTGGTAAGGATGGT

altered gDNA sequence snippet

TGCTTTCCTGCACGCCCTGCAACTGCACTGGTAAGGATGGT

original cDNA sequence snippet

TGCTTTCCTGCACGCCCTGCGACTGCACTGGGTTGAGTTCC

altered cDNA sequence snippet

TGCTTTCCTGCACGCCCTGCAACTGCACTGGGTTGAGTTCC

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

speed

1.32 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: 0.999740836456851 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM023023)
known disease mutation: rs5159 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:138394378C>TN/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.2420G>A
cDNA.2508G>A
g.89928G>A

AA changes

R807Q Score: 43 explain score(s)

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

807

frameshift

known variant

Reference ID: rs28939081

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	2	2

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.334	0.016
	3.482	0.742
(flanking)	0.503	0.723

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
Acc marginally increased	89918	wt: 0.9741 / mu: 0.9784 (marginal change - not scored)	wt: AGGGCCTCTCTGCTTTCCTGCACGCCCTGCGACTGCACTGG mu: AGGGCCTCTCTGCTTTCCTGCACGCCCTGCAACTGCACTGG	ctgc\|ACGC
Donor gained	89924	0.30	mu: ACGCCCTGCAACTGC	GCCC\|tgca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

807

mutated

all conserved

807

Ptroglodytes

all identical

ENSPTRG00000019746

807

Mmulatta

all identical

ENSMMUG00000006547

806

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038600

800

Ggallus

all identical

ENSGALG00000012810

804

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0028671

819

Celegans

all identical

ZK637.8

868

Xtropicalis

all identical

ENSXETG00000011571

805

protein features

start (aa)	end (aa)	feature	details
774	812	TRANSMEM	Helical; (Potential).	lost
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

2420

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

2508

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

89928

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

138394378

original gDNA sequence snippet

TGCTTTCCTGCACGCCCTGCGACTGCACTGGTAAGGATGGT

altered gDNA sequence snippet

TGCTTTCCTGCACGCCCTGCAACTGCACTGGTAAGGATGGT

original cDNA sequence snippet

TGCTTTCCTGCACGCCCTGCGACTGCACTGGGTTGAGTTCC

altered cDNA sequence snippet

TGCTTTCCTGCACGCCCTGCAACTGCACTGGGTTGAGTTCC

wildtype AA sequence

mutated AA sequence

speed

0.94 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999740836456851 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM023023)
known disease mutation: rs5159 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:138394378C>TN/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.2420G>A
cDNA.2658G>A
g.89928G>A

AA changes

R807Q Score: 43 explain score(s)

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

807

frameshift

known variant

Reference ID: rs28939081

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	2	2

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.334	0.016
	3.482	0.742
(flanking)	0.503	0.723

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
Acc marginally increased	89918	wt: 0.9741 / mu: 0.9784 (marginal change - not scored)	wt: AGGGCCTCTCTGCTTTCCTGCACGCCCTGCGACTGCACTGG mu: AGGGCCTCTCTGCTTTCCTGCACGCCCTGCAACTGCACTGG	ctgc\|ACGC
Donor gained	89924	0.30	mu: ACGCCCTGCAACTGC	GCCC\|tgca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

807

mutated

all conserved

807

Ptroglodytes

all identical

ENSPTRG00000019746

807

Mmulatta

all identical

ENSMMUG00000006547

806

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038600

800

Ggallus

all identical

ENSGALG00000012810

804

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0028671

819

Celegans

all identical

ZK637.8

868

Xtropicalis

all identical

ENSXETG00000011571

805

protein features

start (aa)	end (aa)	feature	details
774	812	TRANSMEM	Helical; (Potential).	lost
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

2420

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

2658

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

89928

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

138394378

original gDNA sequence snippet

TGCTTTCCTGCACGCCCTGCGACTGCACTGGTAAGGATGGT

altered gDNA sequence snippet

TGCTTTCCTGCACGCCCTGCAACTGCACTGGTAAGGATGGT

original cDNA sequence snippet

TGCTTTCCTGCACGCCCTGCGACTGCACTGGGTTGAGTTCC

altered cDNA sequence snippet

TGCTTTCCTGCACGCCCTGCAACTGCACTGGGTTGAGTTCC

wildtype AA sequence

mutated AA sequence

speed

0.93 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