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: ENST00000381968
Querying Taster for transcript #2: ENST00000341958
Querying Taster for transcript #3: ENST00000535046
MT speed 0 s - this script 3.883108 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SYT8	polymorphism_automatic	0.999998596515262	simple_aae				T303M	single base exchange	rs484955		show file
SYT8	polymorphism_automatic	0.999998596515262	simple_aae				T289M	single base exchange	rs484955		show file
SYT8	polymorphism_automatic	1	without_aae					single base exchange	rs484955		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.40348473800687e-06 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:1858262C>TN/A show variant in all transcripts IGV

HGNC symbol

SYT8

Ensembl transcript ID

ENST00000381968

Genbank transcript ID

NM_138567

UniProt peptide

Q8NBV8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.908C>T
cDNA.1036C>T
g.9554C>T

AA changes

T303M Score: 81 explain score(s)

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

303

frameshift

known variant

Reference ID: rs484955

database	homozygous (T/T)	heterozygous	allele carriers
1000G	136	657	793
ExAC	1694	14533	16227

regulatory features

H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.629	0.975
	3.451	0.972
(flanking)	-1.845	0.003

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

303

mutated

not conserved

303

Ptroglodytes

all identical

ENSPTRG00000003160

303

Mmulatta

all identical

ENSMMUG00000004837

284

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000031098

299

Ggallus

all identical

ENSGALG00000006602

302

Trubripes

no homologue

Drerio

all identical

ENSDARG00000009564

295

Dmelanogaster

all identical

FBgn0004242

387

Celegans

all identical

F31E8.2

350

Xtropicalis

all identical

ENSXETG00000004623

294

protein features

start (aa)	end (aa)	feature	details
70	401	TOPO_DOM	Cytoplasmic (Potential).	lost
247	346	DOMAIN	C2 2.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1206 / 1206

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

402 / 402

position of stopcodon in wt / mu cDNA

1334 / 1334

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

129 / 129

chromosome

strand

last intron/exon boundary

1095

theoretical NMD boundary in CDS

916

length of CDS

1206

coding sequence (CDS) position

908

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

1036

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

9554

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

1858262

original gDNA sequence snippet

GACAGCCACCAAAAAGGGCACGGCGGCCCCCTACTTCAATG

altered gDNA sequence snippet

GACAGCCACCAAAAAGGGCATGGCGGCCCCCTACTTCAATG

original cDNA sequence snippet

GACAGCCACCAAAAAGGGCACGGCGGCCCCCTACTTCAATG

altered cDNA sequence snippet

GACAGCCACCAAAAAGGGCATGGCGGCCCCCTACTTCAATG

wildtype AA sequence

MLHLHGWQTM QGRKMGHPPV SPSAPAPAGT TAIPGLIPDL VAGTPWPRWA LIAGALAAGV
LLVSCLLCAA CCCCRRHRKK PRDKESVGLG SARGTTTTHL VQPDVDGLES SPGDAQQWGC
LQLSLEFDFG SQEIRVGLRQ AADLRPGGTV DPYARVSVST QAGHRHETKV HRGTLCPVFD
ETCCFHIPQA ELPGATLQVQ LFNFKRFSGH EPLGELRLPL GTVDLQHVLE HWYLLGPPAA
TQPEQVGELC FSLRYVPSSG RLTVVVLEAR GLRPGLAEPY VKVQLMLNQR KWKKRKTATK
KGTAAPYFNE AFTFLVPFSQ VQNVDLVLAV WDRSLPLRTE PVGKVHLGAR ASGQPLQHWA
DMLAHARRPI AQRHPLRPAR EVDRMLALQP RLRLRLPLPH S*

mutated AA sequence

MLHLHGWQTM QGRKMGHPPV SPSAPAPAGT TAIPGLIPDL VAGTPWPRWA LIAGALAAGV
LLVSCLLCAA CCCCRRHRKK PRDKESVGLG SARGTTTTHL VQPDVDGLES SPGDAQQWGC
LQLSLEFDFG SQEIRVGLRQ AADLRPGGTV DPYARVSVST QAGHRHETKV HRGTLCPVFD
ETCCFHIPQA ELPGATLQVQ LFNFKRFSGH EPLGELRLPL GTVDLQHVLE HWYLLGPPAA
TQPEQVGELC FSLRYVPSSG RLTVVVLEAR GLRPGLAEPY VKVQLMLNQR KWKKRKTATK
KGMAAPYFNE AFTFLVPFSQ VQNVDLVLAV WDRSLPLRTE PVGKVHLGAR ASGQPLQHWA
DMLAHARRPI AQRHPLRPAR EVDRMLALQP RLRLRLPLPH S*

speed

0.82 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: 1.40348473800687e-06 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:1858262C>TN/A show variant in all transcripts IGV

HGNC symbol

SYT8

Ensembl transcript ID

ENST00000341958

Genbank transcript ID

N/A

UniProt peptide

Q8NBV8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.866C>T
cDNA.1168C>T
g.9554C>T

AA changes

T289M Score: 81 explain score(s)

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

289

frameshift

known variant

Reference ID: rs484955

database	homozygous (T/T)	heterozygous	allele carriers
1000G	136	657	793
ExAC	1694	14533	16227

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.629	0.975
	3.451	0.972
(flanking)	-1.845	0.003

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

289

mutated

not conserved

289

Ptroglodytes

all identical

ENSPTRG00000003160

303

Mmulatta

all identical

ENSMMUG00000004837

284

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000031098

299

Ggallus

all identical

ENSGALG00000006602

298

Trubripes

no homologue

Drerio

all identical

ENSDARG00000009564

295

Dmelanogaster

all identical

FBgn0004242

387

Celegans

all identical

F31E8.2

350

Xtropicalis

all identical

ENSXETG00000004623

294

protein features

start (aa)	end (aa)	feature	details
70	401	TOPO_DOM	Cytoplasmic (Potential).	lost
247	346	DOMAIN	C2 2.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1164 / 1164

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

388 / 388

position of stopcodon in wt / mu cDNA

1466 / 1466

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

303 / 303

chromosome

strand

last intron/exon boundary

1227

theoretical NMD boundary in CDS

874

length of CDS

1164

coding sequence (CDS) position

866

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

1168

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

9554

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

1858262

original gDNA sequence snippet

GACAGCCACCAAAAAGGGCACGGCGGCCCCCTACTTCAATG

altered gDNA sequence snippet

GACAGCCACCAAAAAGGGCATGGCGGCCCCCTACTTCAATG

original cDNA sequence snippet

GACAGCCACCAAAAAGGGCACGGCGGCCCCCTACTTCAATG

altered cDNA sequence snippet

GACAGCCACCAAAAAGGGCATGGCGGCCCCCTACTTCAATG

wildtype AA sequence

MGHPPVSPSA PAPAGTTAIP GLIPDLVAGT PWPRWALIAG ALAAGVLLVS CLLCAACCCC
RRHRKKPRDK ESVGLGSARG TTTTHLVQPD VDGLESSPGD AQQWGCLQLS LEFDFGSQEI
RVGLRQAADL RPGGTVDPYA RVSVSTQAGH RHETKVHRGT LCPVFDETCC FHIPQAELPG
ATLQVQLFNF KRFSGHEPLG ELRLPLGTVD LQHVLEHWYL LGPPAATQPE QVGELCFSLR
YVPSSGRLTV VVLEARGLRP GLAEPYVKVQ LMLNQRKWKK RKTATKKGTA APYFNEAFTF
LVPFSQVQNV DLVLAVWDRS LPLRTEPVGK VHLGARASGQ PLQHWADMLA HARRPIAQRH
PLRPAREVDR MLALQPRLRL RLPLPHS*

mutated AA sequence

MGHPPVSPSA PAPAGTTAIP GLIPDLVAGT PWPRWALIAG ALAAGVLLVS CLLCAACCCC
RRHRKKPRDK ESVGLGSARG TTTTHLVQPD VDGLESSPGD AQQWGCLQLS LEFDFGSQEI
RVGLRQAADL RPGGTVDPYA RVSVSTQAGH RHETKVHRGT LCPVFDETCC FHIPQAELPG
ATLQVQLFNF KRFSGHEPLG ELRLPLGTVD LQHVLEHWYL LGPPAATQPE QVGELCFSLR
YVPSSGRLTV VVLEARGLRP GLAEPYVKVQ LMLNQRKWKK RKTATKKGMA APYFNEAFTF
LVPFSQVQNV DLVLAVWDRS LPLRTEPVGK VHLGARASGQ PLQHWADMLA HARRPIAQRH
PLRPAREVDR MLALQPRLRL RLPLPHS*

speed

1.05 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 7.78095549209421e-25 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:1858262C>TN/A show variant in all transcripts IGV

HGNC symbol

SYT8

Ensembl transcript ID

ENST00000535046

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.1463C>T
g.9554C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs484955

database	homozygous (T/T)	heterozygous	allele carriers
1000G	136	657	793
ExAC	1694	14533	16227

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.629	0.975
	3.451	0.972
(flanking)	-1.845	0.003

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

poly(A) signal

signal is predicted to be ok

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

last intron/exon boundary

1522

theoretical NMD boundary in CDS

1471

length of CDS

933

coding sequence (CDS) position

N/A

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

1463

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

9554

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

1858262

original gDNA sequence snippet

GACAGCCACCAAAAAGGGCACGGCGGCCCCCTACTTCAATG

altered gDNA sequence snippet

GACAGCCACCAAAAAGGGCATGGCGGCCCCCTACTTCAATG

original cDNA sequence snippet

GACAGCCACCAAAAAGGGCACGGCGGCCCCCTACTTCAATG

altered cDNA sequence snippet

GACAGCCACCAAAAAGGGCATGGCGGCCCCCTACTTCAATG

wildtype AA sequence

MPSSKPGSPA PQDPSPSCRT CSNQVQPGHL LLPLTKASLT GPSPPPAKLG RAQGAPSPKG
PLEIGWSPDA QPLRLGETFL PKGVAQLSRA SSSGHKVGFL QPWPPHPLLP QERVPRHQRQ
CCPRAGPAFG CLRGRPGGWP ATGSGGRQQG RKMGHPPVSP SAPAPAGTTA IPGLIPDLVA
GTPWPRWALI AGALAAGVLL VSCLLCAACC CCRRHRKKPR DKESVGLGSA RGTTTTHLVQ
PDVDGLESSP GDAQQWGCLQ LSLEFDFGSQ EVKGPAAQDQ RFCEFPERVT GEGQTPCPGW
WGADRAGALG *

mutated AA sequence

N/A

speed

0.81 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems