MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000300584
Querying Taster for transcript #2: ENST00000409931
MT speed 0 s - this script 3.793009 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TBC1D2B	polymorphism_automatic	1.16018306073329e-13	simple_aae		affected		A8G	single base exchange	rs7176425		show file
TBC1D2B	polymorphism_automatic	1.16018306073329e-13	simple_aae		affected		A8G	single base exchange	rs7176425		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999884 (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)

chr15:78369972G>CN/A show variant in all transcripts IGV

HGNC symbol

TBC1D2B

Ensembl transcript ID

ENST00000300584

Genbank transcript ID

NM_144572

UniProt peptide

Q9UPU7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.23C>G
cDNA.23C>G
g.95C>G

AA changes

A8G Score: 60 explain score(s)

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

frameshift

known variant

Reference ID: rs7176425

database	homozygous (C/C)	heterozygous	allele carriers
1000G	495	1137	1632
ExAC	1	1	2

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SIX5, Transcription Factor, SIX5 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.238	0.007
	0.212	0.003
(flanking)	-0.237	0

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 gained	94	0.33	mu: CCCGGGGGGAGGAGG	CGGG\|ggga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000009907

n/a

Fcatus

no alignment

ENSFCAG00000010511

n/a

Mmusculus

not conserved

ENSMUSG00000037410

Ggallus

not conserved

ENSGALG00000003322

Trubripes

no alignment

ENSTRUG00000012809

n/a

Drerio

no alignment

ENSDARG00000061986

n/a

Dmelanogaster

no homologue

Celegans

no alignment

ZK1248.10

n/a

Xtropicalis

not conserved

ENSXETG00000009751

protein features

start (aa)	end (aa)	feature	details
34	139	DOMAIN	PH.	might get lost (downstream of altered splice site)
155	155	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
337	535	COILED	Potential.	might get lost (downstream of altered splice site)
511	511	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
662	856	DOMAIN	Rab-GAP TBC.	might get lost (downstream of altered splice site)
949	949	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
957	957	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2892 / 2892

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

964 / 964

position of stopcodon in wt / mu cDNA

2892 / 2892

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

2697

theoretical NMD boundary in CDS

2646

length of CDS

2892

coding sequence (CDS) position

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

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

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

78369972

original gDNA sequence snippet

GCCGGGGGCCGGAGCCCGGGCGGAGGAGGGCGGCGGCGGCG

altered gDNA sequence snippet

GCCGGGGGCCGGAGCCCGGGGGGAGGAGGGCGGCGGCGGCG

original cDNA sequence snippet

GCCGGGGGCCGGAGCCCGGGCGGAGGAGGGCGGCGGCGGCG

altered cDNA sequence snippet

GCCGGGGGCCGGAGCCCGGGGGGAGGAGGGCGGCGGCGGCG

wildtype AA sequence

MPGAGARAEE GGGGGEGAAQ GAAAEPGAGP AREPARLCGY LQKLSGKGPL RGYRSRWFVF
DARRCYLYYF KSPQDALPLG HLDIADACFS YQGPDEAAEP GTEPPAHFQV HSAGAVTVLK
APNRQLMTYW LQELQQKRWE YCNSLDMVKW DSRTSPTPGD FPKGLVARDN TDLIYPHPNA
SAEKARNVLA VETVPGELVG EQAANQPAPG HPNSINFYSL KQWGNELKNS MSSFRPGRGH
NDSRRTVFYT NEEWELLDPT PKDLEESIVQ EEKKKLTPEG NKGVTGSGFP FDFGRNPYKG
KRPLKDIIGS YKNRHSSGDP SSEGTSGSGS VSIRKPASEM QLQVQSQQEE LEQLKKDLSS
QKELVRLLQQ TVRSSQYDKY FTSSRLCEGV PKDTLELLHQ KDDQILGLTS QLERFSLEKE
SLQQEVRTLK SKVGELNEQL GMLMETIQAK DEVIIKLSEG EGNGPPPTVA PSSPSVVPVA
RDQLELDRLK DNLQGYKTQN KFLNKEILEL SALRRNAERR ERDLMAKYSS LEAKLCQIES
KYLILLQEMK TPVCSEDQGP TREVIAQLLE DALQVESQEQ PEQAFVKPHL VSEYDIYGFR
TVPEDDEEEK LVAKVRALDL KTLYLTENQE VSTGVKWENY FASTVNREMM CSPELKNLIR
AGIPHEHRSK VWKWCVDRHT RKFKDNTEPG HFQTLLQKAL EKQNPASKQI ELDLLRTLPN
NKHYSCPTSE GIQKLRNVLL AFSWRNPDIG YCQGLNRLVA VALLYLEQED AFWCLVTIVE
VFMPRDYYTK TLLGSQVDQR VFRDLMSEKL PRLHGHFEQY KVDYTLITFN WFLVVFVDSV
VSDILFKIWD SFLYEGPKVI FRFALALFKY KEEEILKLQD SMSIFKYLRY FTRTILDARK
LISISFGDLN PFPLRQIRNR RAYHLEKVRL ELTELEAIRE DFLRERDTSP DKGELVSDEE
EDT*

mutated AA sequence

MPGAGARGEE GGGGGEGAAQ GAAAEPGAGP AREPARLCGY LQKLSGKGPL RGYRSRWFVF
DARRCYLYYF KSPQDALPLG HLDIADACFS YQGPDEAAEP GTEPPAHFQV HSAGAVTVLK
APNRQLMTYW LQELQQKRWE YCNSLDMVKW DSRTSPTPGD FPKGLVARDN TDLIYPHPNA
SAEKARNVLA VETVPGELVG EQAANQPAPG HPNSINFYSL KQWGNELKNS MSSFRPGRGH
NDSRRTVFYT NEEWELLDPT PKDLEESIVQ EEKKKLTPEG NKGVTGSGFP FDFGRNPYKG
KRPLKDIIGS YKNRHSSGDP SSEGTSGSGS VSIRKPASEM QLQVQSQQEE LEQLKKDLSS
QKELVRLLQQ TVRSSQYDKY FTSSRLCEGV PKDTLELLHQ KDDQILGLTS QLERFSLEKE
SLQQEVRTLK SKVGELNEQL GMLMETIQAK DEVIIKLSEG EGNGPPPTVA PSSPSVVPVA
RDQLELDRLK DNLQGYKTQN KFLNKEILEL SALRRNAERR ERDLMAKYSS LEAKLCQIES
KYLILLQEMK TPVCSEDQGP TREVIAQLLE DALQVESQEQ PEQAFVKPHL VSEYDIYGFR
TVPEDDEEEK LVAKVRALDL KTLYLTENQE VSTGVKWENY FASTVNREMM CSPELKNLIR
AGIPHEHRSK VWKWCVDRHT RKFKDNTEPG HFQTLLQKAL EKQNPASKQI ELDLLRTLPN
NKHYSCPTSE GIQKLRNVLL AFSWRNPDIG YCQGLNRLVA VALLYLEQED AFWCLVTIVE
VFMPRDYYTK TLLGSQVDQR VFRDLMSEKL PRLHGHFEQY KVDYTLITFN WFLVVFVDSV
VSDILFKIWD SFLYEGPKVI FRFALALFKY KEEEILKLQD SMSIFKYLRY FTRTILDARK
LISISFGDLN PFPLRQIRNR RAYHLEKVRL ELTELEAIRE DFLRERDTSP DKGELVSDEE
EDT*

speed

0.89 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: 0.999999999999884 (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)

chr15:78369972G>CN/A show variant in all transcripts IGV

HGNC symbol

TBC1D2B

Ensembl transcript ID

ENST00000409931

Genbank transcript ID

NM_015079

UniProt peptide

Q9UPU7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.23C>G
cDNA.95C>G
g.95C>G

AA changes

A8G Score: 60 explain score(s)

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

frameshift

known variant

Reference ID: rs7176425

database	homozygous (C/C)	heterozygous	allele carriers
1000G	495	1137	1632
ExAC	1	1	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.238	0.007
	0.212	0.003
(flanking)	-0.237	0

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 gained	94	0.33	mu: CCCGGGGGGAGGAGG	CGGG\|ggga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000009907

n/a

Fcatus

no alignment

ENSFCAG00000010511

n/a

Mmusculus

not conserved

ENSMUSG00000037410

Ggallus

not conserved

ENSGALG00000003322

Trubripes

no alignment

ENSTRUG00000012809

n/a

Drerio

no alignment

ENSDARG00000061986

n/a

Dmelanogaster

no homologue

Celegans

no alignment

ZK1248.10

n/a

Xtropicalis

not conserved

ENSXETG00000009751

protein features

start (aa)	end (aa)	feature	details
34	139	DOMAIN	PH.	might get lost (downstream of altered splice site)
155	155	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
337	535	COILED	Potential.	might get lost (downstream of altered splice site)
511	511	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
662	856	DOMAIN	Rab-GAP TBC.	might get lost (downstream of altered splice site)
949	949	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
957	957	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2745 / 2745

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

915 / 915

position of stopcodon in wt / mu cDNA

2817 / 2817

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

73 / 73

chromosome

strand

-1

last intron/exon boundary

2769

theoretical NMD boundary in CDS

2646

length of CDS

2745

coding sequence (CDS) position

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

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

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

78369972

original gDNA sequence snippet

GCCGGGGGCCGGAGCCCGGGCGGAGGAGGGCGGCGGCGGCG

altered gDNA sequence snippet

GCCGGGGGCCGGAGCCCGGGGGGAGGAGGGCGGCGGCGGCG

original cDNA sequence snippet

GCCGGGGGCCGGAGCCCGGGCGGAGGAGGGCGGCGGCGGCG

altered cDNA sequence snippet

GCCGGGGGCCGGAGCCCGGGGGGAGGAGGGCGGCGGCGGCG

wildtype AA sequence

mutated AA sequence

speed

0.90 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems