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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000580223
Querying Taster for transcript #2: ENST00000331427
MT speed 0 s - this script 3.84774 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OTOP2	polymorphism_automatic	9.56348600311685e-09	simple_aae		affected		G465W	single base exchange	rs6501741		show file
OTOP2	polymorphism_automatic	9.56348600311685e-09	simple_aae		affected		G465W	single base exchange	rs6501741		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999990436514 (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)

chr17:72927123G>TN/A show variant in all transcripts IGV

HGNC symbol

OTOP2

Ensembl transcript ID

ENST00000580223

Genbank transcript ID

N/A

UniProt peptide

Q7RTS6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1393G>T
cDNA.1423G>T
g.6754G>T

AA changes

G465W Score: 184 explain score(s)

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

465

frameshift

known variant

Reference ID: rs6501741

database	homozygous (T/T)	heterozygous	allele carriers
1000G	844	1040	1884
ExAC	25503	-18239	7264

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.405	0.004
	-0.126	0
(flanking)	0.75	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
Acc marginally increased	6754	wt: 0.2056 / mu: 0.2206 (marginal change - not scored)	wt: CCGCCTGCCCACCCAACCCCGGGCTGGTTAGCCCCAGCCCT mu: CCGCCTGCCCACCCAACCCCTGGCTGGTTAGCCCCAGCCCT	cccg\|GGCT
Acc increased	6752	wt: 0.30 / mu: 0.56	wt: GTCCGCCTGCCCACCCAACCCCGGGCTGGTTAGCCCCAGCC mu: GTCCGCCTGCCCACCCAACCCCTGGCTGGTTAGCCCCAGCC	accc\|CGGG
Donor gained	6758	0.41	mu: CTGGCTGGTTAGCCC	GGCT\|ggtt

distance from splice site

126

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

465

mutated

not conserved

465

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no alignment

ENSFCAG00000007532

n/a

Mmusculus

not conserved

ENSMUSG00000050201

466

Ggallus

all identical

ENSGALG00000007791

463

VSLRVP

Trubripes

all identical

ENSTRUG00000012018

458

Drerio

not conserved

ENSDARG00000006522

478

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000027433

420

protein features

start (aa)	end (aa)	feature	details
495	515	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
527	547	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1689 / 1689

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

563 / 563

position of stopcodon in wt / mu cDNA

1719 / 1719

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

31 / 31

chromosome

strand

last intron/exon boundary

1549

theoretical NMD boundary in CDS

1468

length of CDS

1689

coding sequence (CDS) position

1393

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

1423

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

6754

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

72927123

original gDNA sequence snippet

CCGCCTGCCCACCCAACCCCGGGCTGGTTAGCCCCAGCCCT

altered gDNA sequence snippet

CCGCCTGCCCACCCAACCCCTGGCTGGTTAGCCCCAGCCCT

original cDNA sequence snippet

CCGCCTGCCCACCCAACCCCGGGCTGGTTAGCCCCAGCCCT

altered cDNA sequence snippet

CCGCCTGCCCACCCAACCCCTGGCTGGTTAGCCCCAGCCCT

wildtype AA sequence

MSEELAQGPK ESPPAPRAGP REVWKKGGRL LSVLLAVNVL LLACTLISGG AFNKVAVYDT
DVFALLTAMM LLATLWILFY LLRTVRCPCA VPYRDAHAGP IWLRGGLVLF GICTLIMDVF
KTGYYSSFFE CQSAIKILHP LIQAVFVIIQ TYFLWVSAKD CVHVHLDLTW CGLMFTLTTN
LAIWMAAVVD ESVHQSHSYS SSHSNASHAR LISDQHADNP VGGDSCLCST AVCQIFQQGY
FYLYPFNIEY SLFASTMLYV MWKNVGRFLA STPGHSHTPT PVSLFRETFF AGPVLGLLLF
VVGLAVFIIY EVQVSGDGSR TRQALVIYYS FNIVCLGLTT LVSLSGSIIY RFDRRAMDHH
KNPTRTLDVA LLMGAALGQY AISYYSIVAV VAGTPQDLLA GLNLTHALLM IAQHTFQNMF
IIESLHRGPP GAEPHSTHPK EPCQDLTFTN LDALHTLSAC PPNPGLVSPS PSDQREAVAI
VSTPRSQWRR QCLKDISLFL LLCNVILWIM PAFGARPHFS NTVEVDFYGY SLWAVIVNIC
LPFGIFYRMH AVSSLLEVYV LS*

mutated AA sequence

MSEELAQGPK ESPPAPRAGP REVWKKGGRL LSVLLAVNVL LLACTLISGG AFNKVAVYDT
DVFALLTAMM LLATLWILFY LLRTVRCPCA VPYRDAHAGP IWLRGGLVLF GICTLIMDVF
KTGYYSSFFE CQSAIKILHP LIQAVFVIIQ TYFLWVSAKD CVHVHLDLTW CGLMFTLTTN
LAIWMAAVVD ESVHQSHSYS SSHSNASHAR LISDQHADNP VGGDSCLCST AVCQIFQQGY
FYLYPFNIEY SLFASTMLYV MWKNVGRFLA STPGHSHTPT PVSLFRETFF AGPVLGLLLF
VVGLAVFIIY EVQVSGDGSR TRQALVIYYS FNIVCLGLTT LVSLSGSIIY RFDRRAMDHH
KNPTRTLDVA LLMGAALGQY AISYYSIVAV VAGTPQDLLA GLNLTHALLM IAQHTFQNMF
IIESLHRGPP GAEPHSTHPK EPCQDLTFTN LDALHTLSAC PPNPWLVSPS PSDQREAVAI
VSTPRSQWRR QCLKDISLFL LLCNVILWIM PAFGARPHFS NTVEVDFYGY SLWAVIVNIC
LPFGIFYRMH AVSSLLEVYV LS*

speed

0.87 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: 0.999999990436514 (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)

chr17:72927123G>TN/A show variant in all transcripts IGV

HGNC symbol

OTOP2

Ensembl transcript ID

ENST00000331427

Genbank transcript ID

NM_178160

UniProt peptide

Q7RTS6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1393G>T
cDNA.1485G>T
g.6754G>T

AA changes

G465W Score: 184 explain score(s)

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

465

frameshift

known variant

Reference ID: rs6501741

database	homozygous (T/T)	heterozygous	allele carriers
1000G	844	1040	1884
ExAC	25503	-18239	7264

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.405	0.004
	-0.126	0
(flanking)	0.75	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
Acc marginally increased	6754	wt: 0.2056 / mu: 0.2206 (marginal change - not scored)	wt: CCGCCTGCCCACCCAACCCCGGGCTGGTTAGCCCCAGCCCT mu: CCGCCTGCCCACCCAACCCCTGGCTGGTTAGCCCCAGCCCT	cccg\|GGCT
Acc increased	6752	wt: 0.30 / mu: 0.56	wt: GTCCGCCTGCCCACCCAACCCCGGGCTGGTTAGCCCCAGCC mu: GTCCGCCTGCCCACCCAACCCCTGGCTGGTTAGCCCCAGCC	accc\|CGGG
Donor gained	6758	0.41	mu: CTGGCTGGTTAGCCC	GGCT\|ggtt

distance from splice site

126

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

465

mutated

not conserved

465

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no alignment

ENSFCAG00000007532

n/a

Mmusculus

not conserved

ENSMUSG00000050201

466

Ggallus

all identical

ENSGALG00000007791

463

VSLRVP

Trubripes

all identical

ENSTRUG00000012018

458

Drerio

not conserved

ENSDARG00000006522

478

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000027433

420

protein features

start (aa)	end (aa)	feature	details
495	515	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
527	547	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1689 / 1689

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

563 / 563

position of stopcodon in wt / mu cDNA

1781 / 1781

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

93 / 93

chromosome

strand

last intron/exon boundary

1611

theoretical NMD boundary in CDS

1468

length of CDS

1689

coding sequence (CDS) position

1393

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

1485

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

6754

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

72927123

original gDNA sequence snippet

CCGCCTGCCCACCCAACCCCGGGCTGGTTAGCCCCAGCCCT

altered gDNA sequence snippet

CCGCCTGCCCACCCAACCCCTGGCTGGTTAGCCCCAGCCCT

original cDNA sequence snippet

CCGCCTGCCCACCCAACCCCGGGCTGGTTAGCCCCAGCCCT

altered cDNA sequence snippet

CCGCCTGCCCACCCAACCCCTGGCTGGTTAGCCCCAGCCCT

wildtype AA sequence

mutated AA sequence

MSEELAQGPK ESPPAPRAGP REVWKKGGRL LSVLLAVNVL LLACTLISGG AFNKVAVYDT
DVFALLTAMM LLATLWILFY LLRTVRCPCA VPYRDAHAGP IWLRGGLVLF GICTLIMDVF
KTGYYSSFFE CQSAIKILHP LIQAVFVIIQ TYFLWVSAKD CVHVHLDLTW CGLMFTLTTN
LAIWMAAVVD ESVHQSHSYS SSHSNASHAR LISDQHADNP VGGDSCLCST AVCQIFQQGY
FYLYPFNIEY SLFASTMLYV MWKNVGRFLA STPGHSHTPT PVSLFRETFF AGPVLGLLLF
VVGLAVFIIY EVQVSGDGSR TRQALVIYYS FNIVCLGLTT LVSLSGSIIY RFDRRAMDHH
KNPTRTLDVA LLMGAALGQY AISYYSIVAV VAGTPQDLLA GLNLTHALLM IAQHTFQNMF
IIESLHRGPP GAEPHSTHPK EPCQDLTFTN LDALHTLSAC PPNPWLVSPS PSDQREAVAI
VSTPRSQWRR QCLKDISLFL LLCNVILWIM PAFGARPHFS NTVEVDFYGY SLWAVIVNIC
LPFGIFYRMH AVSSLLEVYV LS*

speed

0.98 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems