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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000396634
Querying Taster for transcript #2: ENST00000376806
Querying Taster for transcript #3: ENST00000376802
Querying Taster for transcript #4: ENST00000376809
MT speed 0 s - this script 5.484908 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HLA-A	polymorphism_automatic	8.93798125060075e-05	simple_aae		affected		R169H	single base exchange	rs1059520		show file
HLA-A	polymorphism_automatic	8.93798125060075e-05	simple_aae		affected		R169H	single base exchange	rs1059520		show file
HLA-A	polymorphism_automatic	8.93798125060075e-05	simple_aae		affected		R169H	single base exchange	rs1059520		show file
HLA-A	polymorphism_automatic	8.93798125060075e-05	simple_aae		affected		R169H	single base exchange	rs1059520		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999910620187494 (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)

chr6:29911207G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-A

Ensembl transcript ID

ENST00000396634

Genbank transcript ID

NM_002116

UniProt peptide

P10314

alteration type

single base exchange

alteration region

CDS

DNA changes

c.506G>A
cDNA.847G>A
g.2171G>A

AA changes

R169H Score: 29 explain score(s)

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

169

frameshift

known variant

Reference ID: rs1059520

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	3829	25109	28938

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.423	0.626
	-0.086	0.6
(flanking)	0.112	0.643

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 increased	2176	wt: 0.34 / mu: 0.58	wt: GCAAGTGGGAGGCGG mu: ACAAGTGGGAGGCGG	AAGT\|ggga
Donor increased	2175	wt: 0.30 / mu: 0.52	wt: CGCAAGTGGGAGGCG mu: CACAAGTGGGAGGCG	CAAG\|tggg

distance from splice site

114

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

169

mutated

not conserved

169

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000029875

169

Fcatus

no homologue

Mmusculus

no homologue

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
25	308	TOPO_DOM	Extracellular (Potential).	lost
115	206	REGION	Alpha-2.	lost
188	188	DISULFID	By similarity.	might get lost (downstream of altered splice site)
207	298	REGION	Alpha-3.	might get lost (downstream of altered splice site)
209	295	DOMAIN	Ig-like C1-type.	might get lost (downstream of altered splice site)
227	227	DISULFID	By similarity.	might get lost (downstream of altered splice site)
283	283	DISULFID	By similarity.	might get lost (downstream of altered splice site)
299	308	REGION	Connecting peptide.	might get lost (downstream of altered splice site)
309	332	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
333	365	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

1098 / 1098

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

366 / 366

position of stopcodon in wt / mu cDNA

1439 / 1439

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

342 / 342

chromosome

strand

last intron/exon boundary

1435

theoretical NMD boundary in CDS

1043

length of CDS

1098

coding sequence (CDS) position

506

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

847

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

2171

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

29911207

original gDNA sequence snippet

GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG

altered gDNA sequence snippet

GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG

original cDNA sequence snippet

GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG

altered cDNA sequence snippet

GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG

wildtype AA sequence

MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSDRK GGSYTQAASS DSAQGSDVSL
TACKV*

mutated AA sequence

MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKHK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSDRK GGSYTQAASS DSAQGSDVSL
TACKV*

speed

1.17 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: 0.999910620187494 (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)

chr6:29911207G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-A

Ensembl transcript ID

ENST00000376806

Genbank transcript ID

N/A

UniProt peptide

P10314

alteration type

single base exchange

alteration region

CDS

DNA changes

c.506G>A
cDNA.815G>A
g.2171G>A

AA changes

R169H Score: 29 explain score(s)

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

169

frameshift

known variant

Reference ID: rs1059520

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	3829	25109	28938

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.423	0.626
	-0.086	0.6
(flanking)	0.112	0.643

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 increased	2176	wt: 0.34 / mu: 0.58	wt: GCAAGTGGGAGGCGG mu: ACAAGTGGGAGGCGG	AAGT\|ggga
Donor increased	2175	wt: 0.30 / mu: 0.52	wt: CGCAAGTGGGAGGCG mu: CACAAGTGGGAGGCG	CAAG\|tggg

distance from splice site

114

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

169

mutated

not conserved

169

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000029875

169

Fcatus

no homologue

Mmusculus

no homologue

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
25	308	TOPO_DOM	Extracellular (Potential).	lost
115	206	REGION	Alpha-2.	lost
188	188	DISULFID	By similarity.	might get lost (downstream of altered splice site)
207	298	REGION	Alpha-3.	might get lost (downstream of altered splice site)
209	295	DOMAIN	Ig-like C1-type.	might get lost (downstream of altered splice site)
227	227	DISULFID	By similarity.	might get lost (downstream of altered splice site)
283	283	DISULFID	By similarity.	might get lost (downstream of altered splice site)
299	308	REGION	Connecting peptide.	might get lost (downstream of altered splice site)
309	332	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
333	365	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

1116 / 1116

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

372 / 372

position of stopcodon in wt / mu cDNA

1425 / 1425

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

310 / 310

chromosome

strand

last intron/exon boundary

1421

theoretical NMD boundary in CDS

1061

length of CDS

1116

coding sequence (CDS) position

506

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

815

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

2171

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

29911207

original gDNA sequence snippet

GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG

altered gDNA sequence snippet

GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG

original cDNA sequence snippet

GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG

altered cDNA sequence snippet

GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG

wildtype AA sequence

mutated AA sequence

MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKHK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSGGE GVKDRKGGSY TQAASSDSAQ
GSDVSLTACK V*

speed

0.36 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999910620187494 (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)

chr6:29911207G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-A

Ensembl transcript ID

ENST00000376802

Genbank transcript ID

N/A

UniProt peptide

P10314

alteration type

single base exchange

alteration region

CDS

DNA changes

c.506G>A
cDNA.511G>A
g.2171G>A

AA changes

R169H Score: 29 explain score(s)

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

169

frameshift

known variant

Reference ID: rs1059520

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	3829	25109	28938

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.423	0.626
	-0.086	0.6
(flanking)	0.112	0.643

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 increased	2176	wt: 0.34 / mu: 0.58	wt: GCAAGTGGGAGGCGG mu: ACAAGTGGGAGGCGG	AAGT\|ggga
Donor increased	2175	wt: 0.30 / mu: 0.52	wt: CGCAAGTGGGAGGCG mu: CACAAGTGGGAGGCG	CAAG\|tggg

distance from splice site

114

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

169

mutated

not conserved

169

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000029875

169

Fcatus

no homologue

Mmusculus

no homologue

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
25	308	TOPO_DOM	Extracellular (Potential).	lost
115	206	REGION	Alpha-2.	lost
188	188	DISULFID	By similarity.	might get lost (downstream of altered splice site)
207	298	REGION	Alpha-3.	might get lost (downstream of altered splice site)
209	295	DOMAIN	Ig-like C1-type.	might get lost (downstream of altered splice site)
227	227	DISULFID	By similarity.	might get lost (downstream of altered splice site)
283	283	DISULFID	By similarity.	might get lost (downstream of altered splice site)
299	308	REGION	Connecting peptide.	might get lost (downstream of altered splice site)
309	332	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
333	365	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

900 / 900

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

300 / 300

position of stopcodon in wt / mu cDNA

905 / 905

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

6 / 6

chromosome

strand

last intron/exon boundary

901

theoretical NMD boundary in CDS

845

length of CDS

900

coding sequence (CDS) position

506

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

511

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

2171

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

29911207

original gDNA sequence snippet

GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG

altered gDNA sequence snippet

GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG

original cDNA sequence snippet

GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG

altered cDNA sequence snippet

GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG

wildtype AA sequence

mutated AA sequence

MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKHK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWV*

speed

1.18 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999910620187494 (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)

chr6:29911207G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-A

Ensembl transcript ID

ENST00000376809

Genbank transcript ID

N/A

UniProt peptide

P10314

alteration type

single base exchange

alteration region

CDS

DNA changes

c.506G>A
cDNA.528G>A
g.2171G>A

AA changes

R169H Score: 29 explain score(s)

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

169

frameshift

known variant

Reference ID: rs1059520

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	3829	25109	28938

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.423	0.626
	-0.086	0.6
(flanking)	0.112	0.643

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 increased	2176	wt: 0.34 / mu: 0.58	wt: GCAAGTGGGAGGCGG mu: ACAAGTGGGAGGCGG	AAGT\|ggga
Donor increased	2175	wt: 0.30 / mu: 0.52	wt: CGCAAGTGGGAGGCG mu: CACAAGTGGGAGGCG	CAAG\|tggg

distance from splice site

114

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

169

mutated

not conserved

169

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000029875

169

Fcatus

no homologue

Mmusculus

no homologue

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
25	308	TOPO_DOM	Extracellular (Potential).	lost
115	206	REGION	Alpha-2.	lost
188	188	DISULFID	By similarity.	might get lost (downstream of altered splice site)
207	298	REGION	Alpha-3.	might get lost (downstream of altered splice site)
209	295	DOMAIN	Ig-like C1-type.	might get lost (downstream of altered splice site)
227	227	DISULFID	By similarity.	might get lost (downstream of altered splice site)
283	283	DISULFID	By similarity.	might get lost (downstream of altered splice site)
299	308	REGION	Connecting peptide.	might get lost (downstream of altered splice site)
309	332	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
333	365	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

1098 / 1098

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

366 / 366

position of stopcodon in wt / mu cDNA

1120 / 1120

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

1116

theoretical NMD boundary in CDS

1043

length of CDS

1098

coding sequence (CDS) position

506

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

528

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

2171

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

29911207

original gDNA sequence snippet

GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG

altered gDNA sequence snippet

GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG

original cDNA sequence snippet

GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG

altered cDNA sequence snippet

GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG

wildtype AA sequence

mutated AA sequence

MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKHK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSDRK GGSYTQAASS DSAQGSDVSL
TACKV*

speed

1.10 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems