MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000380252
Querying Taster for transcript #2: ENST00000380259
Querying Taster for transcript #3: ENST00000380237
Querying Taster for transcript #4: ENST00000396895
Querying Taster for transcript #5: ENST00000380219
MT speed 0 s - this script 3.081121 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR51B6	polymorphism_automatic	4.5582735996863e-07	simple_aae		affected		S126N	single base exchange	rs5006888		show file
HBG2	polymorphism_automatic	0.157515962906963	without_aae					single base exchange	rs5006888		show file
HBG2	polymorphism_automatic	0.157515962906963	without_aae					single base exchange	rs5006888		show file
HBE1	polymorphism_automatic	0.157515962906963	without_aae					single base exchange	rs5006888		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999954417264 (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)

chr11:5373114G>AN/A show variant in all transcripts IGV

HGNC symbol

OR51B6

Ensembl transcript ID

ENST00000380219

Genbank transcript ID

NM_001004750

UniProt peptide

Q9H340

alteration type

single base exchange

alteration region

CDS

DNA changes

c.377G>A
cDNA.377G>A
g.377G>A

AA changes

S126N Score: 46 explain score(s)

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

126

frameshift

known variant

Reference ID: rs5006888

database	homozygous (A/A)	heterozygous	allele carriers
1000G	942	1153	2095
ExAC	22245	-11723	10522

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.574	0.373
	0.136	0.411
(flanking)	0.853	0.761

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 marginally increased	380	wt: 0.9280 / mu: 0.9358 (marginal change - not scored)	wt: CAGCCCCTTAAGATA mu: CAACCCCTTAAGATA	GCCC\|ctta
Donor gained	373	0.47	mu: CCATCCGCAACCCCT	ATCC\|gcaa

distance from splice site

377

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

126

mutated

all conserved

126

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000047163

129

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000016607

129

protein features

start (aa)	end (aa)	feature	details
119	137	TOPO_DOM	Cytoplasmic (Potential).	lost
123	126	CONFLICT	TIRS -> AIHN (in Ref. 1; AAG41682).	lost
138	158	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
159	194	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
187	187	DISULFID	By similarity.	might get lost (downstream of altered splice site)
195	215	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
216	235	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
236	256	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
257	271	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
272	292	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
293	312	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

939 / 939

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

313 / 313

position of stopcodon in wt / mu cDNA

939 / 939

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

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

939

coding sequence (CDS) position

377

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

377

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

377

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

5373114

original gDNA sequence snippet

CTGTTTCATTACCATCCGCAGCCCCTTAAGATATACCTCTA

altered gDNA sequence snippet

CTGTTTCATTACCATCCGCAACCCCTTAAGATATACCTCTA

original cDNA sequence snippet

CTGTTTCATTACCATCCGCAGCCCCTTAAGATATACCTCTA

altered cDNA sequence snippet

CTGTTTCATTACCATCCGCAACCCCTTAAGATATACCTCTA

wildtype AA sequence

MGLNKSASTF QLTGFPGMEK AHHWIFIPLL AAYISILLGN GTLLFLIRND HNLHEPMYYF
LAMLAATDLG VTLTTMPTVL GVLWLDHREI GHGACFSQAY FIHTLSVMES GVLLAMAYDC
FITIRSPLRY TSILTNTQVM KIGVRVLTRA GLSIMPIVVR LHWFPYCRSH VLSHAFCLHQ
DVIKLACADI TFNRLYPVVV LFAMVLLDFL IIFFSYILIL KTVMGIGSGG ERAKALNTCV
SHICCILVFY VTVVCLTFIH RFGKHVPHVV HITMSYIHFL FPPFMNPFIY SIKTKQIQSG
ILRLFSLPHS RA*

mutated AA sequence

MGLNKSASTF QLTGFPGMEK AHHWIFIPLL AAYISILLGN GTLLFLIRND HNLHEPMYYF
LAMLAATDLG VTLTTMPTVL GVLWLDHREI GHGACFSQAY FIHTLSVMES GVLLAMAYDC
FITIRNPLRY TSILTNTQVM KIGVRVLTRA GLSIMPIVVR LHWFPYCRSH VLSHAFCLHQ
DVIKLACADI TFNRLYPVVV LFAMVLLDFL IIFFSYILIL KTVMGIGSGG ERAKALNTCV
SHICCILVFY VTVVCLTFIH RFGKHVPHVV HITMSYIHFL FPPFMNPFIY SIKTKQIQSG
ILRLFSLPHS RA*

speed

0.25 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: without_aae, prob: 0.842484037093037 (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)

chr11:5373114G>AN/A show variant in all transcripts IGV

HGNC symbol

HBG2

Ensembl transcript ID

ENST00000380252

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.293906C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs5006888

database	homozygous (A/A)	heterozygous	allele carriers
1000G	942	1153	2095
ExAC	22245	-11723	10522

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.574	0.373
	0.136	0.411
(flanking)	0.853	0.761

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

97370

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

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

194 / 194

chromosome

strand

-1

last intron/exon boundary

479

theoretical NMD boundary in CDS

235

length of CDS

414

coding sequence (CDS) position

N/A

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

N/A

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

293906

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

5373114

original gDNA sequence snippet

TAGAGGTATATCTTAAGGGGCTGCGGATGGTAATGAAACAG

altered gDNA sequence snippet

TAGAGGTATATCTTAAGGGGTTGCGGATGGTAATGAAACAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVVLGEMKRK VLPLHFLPFM RLLVVYPWTQ RFFDSFGNLS SASAIMGNPK VKAHGKKVLT
SLGDAIKHLD DLKGTFAQLS ELHCDKLHVD PENFKLLGNV LVTVLAIHFG KEFTPEVQAS
WQKMVTGVAS ALSSRYH*

mutated AA sequence

N/A

speed

0.67 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.842484037093037 (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)

chr11:5373114G>AN/A show variant in all transcripts IGV

HGNC symbol

HBG2

Ensembl transcript ID

ENST00000380259

Genbank transcript ID

NM_000184

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.293906C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs5006888

database	homozygous (A/A)	heterozygous	allele carriers
1000G	942	1153	2095
ExAC	22245	-11723	10522

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.574	0.373
	0.136	0.411
(flanking)	0.853	0.761

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

5985

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

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

1242 / 1242

chromosome

strand

-1

last intron/exon boundary

1557

theoretical NMD boundary in CDS

265

length of CDS

444

coding sequence (CDS) position

N/A

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

N/A

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

293906

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

5373114

original gDNA sequence snippet

TAGAGGTATATCTTAAGGGGCTGCGGATGGTAATGAAACAG

altered gDNA sequence snippet

TAGAGGTATATCTTAAGGGGTTGCGGATGGTAATGAAACAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MGHFTEEDKA TITSLWGKVN VEDAGGETLG RLLVVYPWTQ RFFDSFGNLS SASAIMGNPK
VKAHGKKVLT SLGDAIKHLD DLKGTFAQLS ELHCDKLHVD PENFKLLGNV LVTVLAIHFG
KEFTPEVQAS WQKMVTGVAS ALSSRYH*

mutated AA sequence

N/A

speed

0.23 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.842484037093037 (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)

chr11:5373114G>AN/A show variant in all transcripts IGV

HGNC symbol

HBE1

Ensembl transcript ID

ENST00000380237

Genbank transcript ID

NM_005330

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.153734C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs5006888

database	homozygous (A/A)	heterozygous	allele carriers
1000G	942	1153	2095
ExAC	22245	-11723	10522

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.574	0.373
	0.136	0.411
(flanking)	0.853	0.761

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

69933

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

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

346 / 346

chromosome

strand

-1

last intron/exon boundary

661

theoretical NMD boundary in CDS

265

length of CDS

444

coding sequence (CDS) position

N/A

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

N/A

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

153734

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

5373114

original gDNA sequence snippet

TAGAGGTATATCTTAAGGGGCTGCGGATGGTAATGAAACAG

altered gDNA sequence snippet

TAGAGGTATATCTTAAGGGGTTGCGGATGGTAATGAAACAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVHFTAEEKA AVTSLWSKMN VEEAGGEALG RLLVVYPWTQ RFFDSFGNLS SPSAILGNPK
VKAHGKKVLT SFGDAIKNMD NLKPAFAKLS ELHCDKLHVD PENFKLLGNV MVIILATHFG
KEFTPEVQAA WQKLVSAVAI ALAHKYH*

mutated AA sequence

N/A

speed

0.21 s

Problems

annotation problem

The chosen transcript ENST00000396895 on chromosome 11 has no correct in-frame stop codon (TGA, TAA or TAG) annotated
This is likely to cause a false prediction. You should choose another transcript.

back to results table