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 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: ENST00000322641
MT speed 0 s - this script 4.133909 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR52D1	polymorphism_automatic	0.996760520221715	simple_aae				I251T	single base exchange	rs7101919		show file
HBG2	polymorphism_automatic	1	without_aae		affected			single base exchange	rs7101919		show file
HBG2	polymorphism_automatic	1	without_aae		affected			single base exchange	rs7101919		show file
HBE1	polymorphism_automatic	1	without_aae		affected			single base exchange	rs7101919		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00323947977828479 (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)

chr11:5510688T>CN/A show variant in all transcripts IGV

HGNC symbol

OR52D1

Ensembl transcript ID

ENST00000322641

Genbank transcript ID

NM_001005163

UniProt peptide

Q9H346

alteration type

single base exchange

alteration region

CDS

DNA changes

c.752T>C
cDNA.774T>C
g.774T>C

AA changes

I251T Score: 89 explain score(s)

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

251

frameshift

known variant

Reference ID: rs7101919

database	homozygous (C/C)	heterozygous	allele carriers
1000G	101	571	672
ExAC	4797	22089	26886

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.246	0.989
	4.836	0.989
(flanking)	-0.557	0.001

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	767	wt: 0.7180 / mu: 0.7277 (marginal change - not scored)	wt: GTACCTGTGGCTCCCACATTGGCATCATCCTGGTTTTCTAC mu: GTACCTGTGGCTCCCACATTGGCATCACCCTGGTTTTCTAC	attg\|GCAT

distance from splice site

292

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

251

mutated

not conserved

251

Ptroglodytes

all identical

ENSPTRG00000003252

251

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000010729

251

Mmusculus

all identical

ENSMUSG00000073931

245

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
241	261	TRANSMEM	Helical; Name=6; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

957 / 957

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

319 / 319

position of stopcodon in wt / mu cDNA

979 / 979

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

23 / 23

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

957

coding sequence (CDS) position

752

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

774

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

774

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

5510688

original gDNA sequence snippet

TGGCTCCCACATTGGCATCATCCTGGTTTTCTACATCCCTG

altered gDNA sequence snippet

TGGCTCCCACATTGGCATCACCCTGGTTTTCTACATCCCTG

original cDNA sequence snippet

TGGCTCCCACATTGGCATCATCCTGGTTTTCTACATCCCTG

altered cDNA sequence snippet

TGGCTCCCACATTGGCATCACCCTGGTTTTCTACATCCCTG

wildtype AA sequence

MSDSNLSDNH LPDTFFLTGI PGLEAAHFWI AIPFCAMYLV ALVGNAALIL VIAMDNALHA
PMYLFLCLLS LTDLALSSTT VPKMLAILWL HAGEISFGGC LAQMFCVHSI YALESSILLA
MAFDRYVAIC NPLRYTTILN HAVIGRIGFV GLFRSVAIVS PFIFLLRRLP YCGHRVMTHT
YCEHMGIARL ACANITVNIV YGLTVALLAM GLDSILIAIS YGFILHAVFH LPSHDAQHKA
LSTCGSHIGI ILVFYIPAFF SFLTHRFGHH EVPKHVHIFL ANLYVLVPPV LNPILYGART
KEIRSRLLKL LHLGKTSI*

mutated AA sequence

MSDSNLSDNH LPDTFFLTGI PGLEAAHFWI AIPFCAMYLV ALVGNAALIL VIAMDNALHA
PMYLFLCLLS LTDLALSSTT VPKMLAILWL HAGEISFGGC LAQMFCVHSI YALESSILLA
MAFDRYVAIC NPLRYTTILN HAVIGRIGFV GLFRSVAIVS PFIFLLRRLP YCGHRVMTHT
YCEHMGIARL ACANITVNIV YGLTVALLAM GLDSILIAIS YGFILHAVFH LPSHDAQHKA
LSTCGSHIGI TLVFYIPAFF SFLTHRFGHH EVPKHVHIFL ANLYVLVPPV LNPILYGART
KEIRSRLLKL LHLGKTSI*

speed

0.74 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: 5.74328174980851e-44 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr11:5510688T>CN/A show variant in all transcripts IGV

HGNC symbol

HBG2

Ensembl transcript ID

ENST00000380252

Genbank transcript ID

N/A

UniProt peptide

P69892

alteration type

single base exchange

alteration region

intron

DNA changes

g.156332A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7101919

database	homozygous (C/C)	heterozygous	allele carriers
1000G	101	571	672
ExAC	4797	22089	26886

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.246	0.989
	4.836	0.989
(flanking)	-0.557	0.001

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	156325	wt: 0.3230 / mu: 0.3402 (marginal change - not scored)	wt: TAGAAAACCAGGATG mu: TAGAAAACCAGGGTG	GAAA\|acca
Donor marginally increased	156337	wt: 0.7197 / mu: 0.7296 (marginal change - not scored)	wt: ATGATGCCAATGTGG mu: GTGATGCCAATGTGG	GATG\|ccaa
Donor increased	156331	wt: 0.25 / mu: 0.97	wt: ACCAGGATGATGCCA mu: ACCAGGGTGATGCCA	CAGG\|atga
Donor marginally increased	156329	wt: 0.2085 / mu: 0.2156 (marginal change - not scored)	wt: AAACCAGGATGATGC mu: AAACCAGGGTGATGC	ACCA\|ggat
Donor gained	156326	0.82	mu: AGAAAACCAGGGTGA	AAAA\|ccag

distance from splice site

15893

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
21	35	HELIX		might get lost (downstream of altered splice site)
36	36	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
40	42	HELIX		might get lost (downstream of altered splice site)
52	56	HELIX		might get lost (downstream of altered splice site)
59	76	HELIX		might get lost (downstream of altered splice site)
64	64	METAL	Iron (heme distal ligand).	might get lost (downstream of altered splice site)
77	80	TURN		might get lost (downstream of altered splice site)
82	95	HELIX		might get lost (downstream of altered splice site)
93	93	METAL	Iron (heme proximal ligand).	might get lost (downstream of altered splice site)
102	119	HELIX		might get lost (downstream of altered splice site)
120	122	HELIX		might get lost (downstream of altered splice site)
125	143	HELIX		might get lost (downstream of altered splice site)

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)

156332

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

5510688

original gDNA sequence snippet

CAGGGATGTAGAAAACCAGGATGATGCCAATGTGGGAGCCA

altered gDNA sequence snippet

CAGGGATGTAGAAAACCAGGGTGATGCCAATGTGGGAGCCA

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

0.69 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 5.74328174980851e-44 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr11:5510688T>CN/A show variant in all transcripts IGV

HGNC symbol

HBG2

Ensembl transcript ID

ENST00000380259

Genbank transcript ID

NM_000184

UniProt peptide

P69892

alteration type

single base exchange

alteration region

intron

DNA changes

g.156332A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7101919

database	homozygous (C/C)	heterozygous	allele carriers
1000G	101	571	672
ExAC	4797	22089	26886

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.246	0.989
	4.836	0.989
(flanking)	-0.557	0.001

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

splice sites

splice site change before start ATG (at aa -187) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	156325	wt: 0.3230 / mu: 0.3402 (marginal change - not scored)	wt: TAGAAAACCAGGATG mu: TAGAAAACCAGGGTG	GAAA\|acca
Donor marginally increased	156337	wt: 0.7197 / mu: 0.7296 (marginal change - not scored)	wt: ATGATGCCAATGTGG mu: GTGATGCCAATGTGG	GATG\|ccaa
Donor increased	156331	wt: 0.25 / mu: 0.97	wt: ACCAGGATGATGCCA mu: ACCAGGGTGATGCCA	CAGG\|atga
Donor marginally increased	156329	wt: 0.2085 / mu: 0.2156 (marginal change - not scored)	wt: AAACCAGGATGATGC mu: AAACCAGGGTGATGC	ACCA\|ggat
Donor gained	156326	0.82	mu: AGAAAACCAGGGTGA	AAAA\|ccag

distance from splice site

99999

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	1	INIT_MET	Removed.	might get lost (downstream of altered splice site)
2	2	MOD_RES	N-acetylglycine; in form Hb F1.	might get lost (downstream of altered splice site)
6	15	HELIX		might get lost (downstream of altered splice site)
16	18	HELIX		might get lost (downstream of altered splice site)
21	35	HELIX		might get lost (downstream of altered splice site)
36	36	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
40	42	HELIX		might get lost (downstream of altered splice site)
52	56	HELIX		might get lost (downstream of altered splice site)
59	76	HELIX		might get lost (downstream of altered splice site)
64	64	METAL	Iron (heme distal ligand).	might get lost (downstream of altered splice site)
77	80	TURN		might get lost (downstream of altered splice site)
82	95	HELIX		might get lost (downstream of altered splice site)
93	93	METAL	Iron (heme proximal ligand).	might get lost (downstream of altered splice site)
102	119	HELIX		might get lost (downstream of altered splice site)
120	122	HELIX		might get lost (downstream of altered splice site)
125	143	HELIX		might get lost (downstream of altered splice site)

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)

156332

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

5510688

original gDNA sequence snippet

CAGGGATGTAGAAAACCAGGATGATGCCAATGTGGGAGCCA

altered gDNA sequence snippet

CAGGGATGTAGAAAACCAGGGTGATGCCAATGTGGGAGCCA

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

0.63 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 5.74328174980851e-44 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr11:5510688T>CN/A show variant in all transcripts IGV

HGNC symbol

HBE1

Ensembl transcript ID

ENST00000380237

Genbank transcript ID

NM_005330

UniProt peptide

P02100

alteration type

single base exchange

alteration region

intron

DNA changes

g.16160A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7101919

database	homozygous (C/C)	heterozygous	allele carriers
1000G	101	571	672
ExAC	4797	22089	26886

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.246	0.989
	4.836	0.989
(flanking)	-0.557	0.001

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

splice sites

splice site change before start ATG (at aa -102) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	16159	wt: 0.25 / mu: 0.97	wt: ACCAGGATGATGCCA mu: ACCAGGGTGATGCCA	CAGG\|atga
Donor marginally increased	16165	wt: 0.7197 / mu: 0.7296 (marginal change - not scored)	wt: ATGATGCCAATGTGG mu: GTGATGCCAATGTGG	GATG\|ccaa
Donor marginally increased	16157	wt: 0.2085 / mu: 0.2156 (marginal change - not scored)	wt: AAACCAGGATGATGC mu: AAACCAGGGTGATGC	ACCA\|ggat
Donor marginally increased	16153	wt: 0.3230 / mu: 0.3402 (marginal change - not scored)	wt: TAGAAAACCAGGATG mu: TAGAAAACCAGGGTG	GAAA\|acca
Donor gained	16154	0.82	mu: AGAAAACCAGGGTGA	AAAA\|ccag

distance from splice site

16111

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	1	INIT_MET	Removed.	might get lost (downstream of altered splice site)
6	18	HELIX		might get lost (downstream of altered splice site)
21	23	TURN		might get lost (downstream of altered splice site)
24	35	HELIX		might get lost (downstream of altered splice site)
36	36	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
37	41	HELIX		might get lost (downstream of altered splice site)
44	46	HELIX		might get lost (downstream of altered splice site)
52	57	HELIX		might get lost (downstream of altered splice site)
59	76	HELIX		might get lost (downstream of altered splice site)
64	64	METAL	Iron (heme distal ligand).	might get lost (downstream of altered splice site)
79	81	STRAND		might get lost (downstream of altered splice site)
83	86	TURN		might get lost (downstream of altered splice site)
87	94	HELIX		might get lost (downstream of altered splice site)
93	93	METAL	Iron (heme proximal ligand).	might get lost (downstream of altered splice site)
95	97	TURN		might get lost (downstream of altered splice site)
102	119	HELIX		might get lost (downstream of altered splice site)
120	122	HELIX		might get lost (downstream of altered splice site)
125	142	HELIX		might get lost (downstream of altered splice site)
143	143	CONFLICT	A -> G (in Ref. 5; AA sequence).	might get lost (downstream of altered splice site)

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)

16160

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

5510688

original gDNA sequence snippet

CAGGGATGTAGAAAACCAGGATGATGCCAATGTGGGAGCCA

altered gDNA sequence snippet

CAGGGATGTAGAAAACCAGGGTGATGCCAATGTGGGAGCCA

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

0.68 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