MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000376228
Querying Taster for transcript #2: ENST00000383329
Querying Taster for transcript #3: ENST00000396254
Querying Taster for transcript #4: ENST00000539307
MT speed 0 s - this script 5.906686 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HLA-C	polymorphism_automatic	3.62043728330264e-13	simple_aae				A97T	single base exchange	rs41543814		show file
HLA-C	polymorphism_automatic	3.62043728330264e-13	simple_aae				A97T	single base exchange	rs41543814		show file
HLA-C	polymorphism_automatic	3.62043728330264e-13	simple_aae				A97T	single base exchange	rs41543814		show file
HLA-C	polymorphism_automatic	3.62043728330264e-13	simple_aae				A134T	single base exchange	rs41543814		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999638 (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)

chr6:31239430C>TN/A show variant in all transcripts IGV

HGNC symbol

HLA-C

Ensembl transcript ID

ENST00000383329

Genbank transcript ID

N/A

UniProt peptide

P30501

alteration type

single base exchange

alteration region

CDS

DNA changes

c.289G>A
cDNA.304G>A
g.478G>A

AA changes

A97T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs41543814

database	homozygous (T/T)	heterozygous	allele carriers
1000G	561	1192	1753
ExAC	11836	9095	20931

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-6.291	0
	-1.034	0
(flanking)	0.226	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	470	wt: 0.8588 / mu: 0.8611 (marginal change - not scored)	wt: GCGCCAGGCACAGGC mu: GCGCCAGGCACAGAC	GCCA\|ggca
Donor marginally increased	481	wt: 0.8632 / mu: 0.9403 (marginal change - not scored)	wt: AGGCTGACCGAGTGA mu: AGACTGACCGAGTGA	GCTG\|accg
Donor marginally increased	471	wt: 0.7342 / mu: 0.7576 (marginal change - not scored)	wt: CGCCAGGCACAGGCT mu: CGCCAGGCACAGACT	CCAG\|gcac

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

all identical

ENSPTRG00000041261

Mmulatta

not conserved

ENSMMUG00000029841

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	114	REGION	Alpha-1.	lost
25	308	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1119 / 1119

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

373 / 373

position of stopcodon in wt / mu cDNA

1134 / 1134

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

16 / 16

chromosome

strand

-1

last intron/exon boundary

1130

theoretical NMD boundary in CDS

1064

length of CDS

1119

coding sequence (CDS) position

289

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

304

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

478

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

31239430

original gDNA sequence snippet

AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG

altered gDNA sequence snippet

AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG

original cDNA sequence snippet

AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG

altered cDNA sequence snippet

AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG

wildtype AA sequence

MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGH FLPTGGKGGS CSQAACSNSA
QGSDESLITC KA*

mutated AA sequence

MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQTDRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGH FLPTGGKGGS CSQAACSNSA
QGSDESLITC KA*

speed

1.31 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: 0.999999999999638 (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)

chr6:31239430C>TN/A show variant in all transcripts IGV

HGNC symbol

HLA-C

Ensembl transcript ID

ENST00000396254

Genbank transcript ID

N/A

UniProt peptide

P30501

alteration type

single base exchange

alteration region

CDS

DNA changes

c.289G>A
cDNA.304G>A
g.478G>A

AA changes

A97T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs41543814

database	homozygous (T/T)	heterozygous	allele carriers
1000G	561	1192	1753
ExAC	11836	9095	20931

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-6.291	0
	-1.034	0
(flanking)	0.226	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	470	wt: 0.8588 / mu: 0.8611 (marginal change - not scored)	wt: GCGCCAGGCACAGGC mu: GCGCCAGGCACAGAC	GCCA\|ggca
Donor marginally increased	481	wt: 0.8632 / mu: 0.9403 (marginal change - not scored)	wt: AGGCTGACCGAGTGA mu: AGACTGACCGAGTGA	GCTG\|accg
Donor marginally increased	471	wt: 0.7342 / mu: 0.7576 (marginal change - not scored)	wt: CGCCAGGCACAGGCT mu: CGCCAGGCACAGACT	CCAG\|gcac

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

all identical

ENSPTRG00000041261

Mmulatta

not conserved

ENSMMUG00000029841

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	114	REGION	Alpha-1.	lost
25	308	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1194 / 1194

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

398 / 398

position of stopcodon in wt / mu cDNA

1209 / 1209

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

16 / 16

chromosome

strand

-1

last intron/exon boundary

1108

theoretical NMD boundary in CDS

1042

length of CDS

1194

coding sequence (CDS) position

289

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

304

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

478

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

31239430

original gDNA sequence snippet

AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG

altered gDNA sequence snippet

AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG

original cDNA sequence snippet

AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG

altered cDNA sequence snippet

AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG

wildtype AA sequence

mutated AA sequence

speed

1.32 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999638 (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)

chr6:31239430C>TN/A show variant in all transcripts IGV

HGNC symbol

HLA-C

Ensembl transcript ID

ENST00000376228

Genbank transcript ID

NM_002117

UniProt peptide

P30501

alteration type

single base exchange

alteration region

CDS

DNA changes

c.289G>A
cDNA.304G>A
g.478G>A

AA changes

A97T Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs41543814

database	homozygous (T/T)	heterozygous	allele carriers
1000G	561	1192	1753
ExAC	11836	9095	20931

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-6.291	0
	-1.034	0
(flanking)	0.226	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	470	wt: 0.8588 / mu: 0.8611 (marginal change - not scored)	wt: GCGCCAGGCACAGGC mu: GCGCCAGGCACAGAC	GCCA\|ggca
Donor marginally increased	481	wt: 0.8632 / mu: 0.9403 (marginal change - not scored)	wt: AGGCTGACCGAGTGA mu: AGACTGACCGAGTGA	GCTG\|accg
Donor marginally increased	471	wt: 0.7342 / mu: 0.7576 (marginal change - not scored)	wt: CGCCAGGCACAGGCT mu: CGCCAGGCACAGACT	CCAG\|gcac

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

all identical

ENSPTRG00000041261

Mmulatta

not conserved

ENSMMUG00000029841

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	114	REGION	Alpha-1.	lost
25	308	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1101 / 1101

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

367 / 367

position of stopcodon in wt / mu cDNA

1116 / 1116

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

16 / 16

chromosome

strand

-1

last intron/exon boundary

1112

theoretical NMD boundary in CDS

1046

length of CDS

1101

coding sequence (CDS) position

289

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

304

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

478

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

31239430

original gDNA sequence snippet

AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG

altered gDNA sequence snippet

AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG

original cDNA sequence snippet

AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG

altered cDNA sequence snippet

AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG

wildtype AA sequence

mutated AA sequence

speed

1.34 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999638 (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)

chr6:31239430C>TN/A show variant in all transcripts IGV

HGNC symbol

HLA-C

Ensembl transcript ID

ENST00000539307

Genbank transcript ID

N/A

UniProt peptide

P30501

alteration type

single base exchange

alteration region

CDS

DNA changes

c.400G>A
cDNA.400G>A
g.478G>A

AA changes

A134T Score: 58 explain score(s)

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

134

frameshift

known variant

Reference ID: rs41543814

database	homozygous (T/T)	heterozygous	allele carriers
1000G	561	1192	1753
ExAC	11836	9095	20931

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-6.291	0
	-1.034	0
(flanking)	0.226	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	470	wt: 0.8588 / mu: 0.8611 (marginal change - not scored)	wt: GCGCCAGGCACAGGC mu: GCGCCAGGCACAGAC	GCCA\|ggca
Donor marginally increased	481	wt: 0.8632 / mu: 0.9403 (marginal change - not scored)	wt: AGGCTGACCGAGTGA mu: AGACTGACCGAGTGA	GCTG\|accg
Donor marginally increased	471	wt: 0.7342 / mu: 0.7576 (marginal change - not scored)	wt: CGCCAGGCACAGGCT mu: CGCCAGGCACAGACT	CCAG\|gcac

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

134

mutated

not conserved

134

Ptroglodytes

all identical

ENSPTRG00000041261

Mmulatta

not conserved

ENSMMUG00000029841

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

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1212 / 1212

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

404 / 404

position of stopcodon in wt / mu cDNA

1212 / 1212

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

1208

theoretical NMD boundary in CDS

1157

length of CDS

1212

coding sequence (CDS) position

400

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

400

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

478

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

31239430

original gDNA sequence snippet

AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG

altered gDNA sequence snippet

AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG

original cDNA sequence snippet

AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG

altered cDNA sequence snippet

AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG

wildtype AA sequence

MRVMAPRALL LLLSGGLALT ETWACECGVG REAASAERSE GPPGEPRREV GRAGLSPSSP
PGSHSMRYFD TAVSRPGRGE PRFISVGYVD DTQFVRFDSD AASPRGEPRA PWVEQEGPEY
WDRETQKYKR QAQADRVSLR NLRGYYNQSE DGSHTLQRMS GCDLGPDGRL LRGYDQSAYD
GKDYIALNED LRSWTAADTA AQITQRKLEA ARAAEQLRAY LEGTCVEWLR RYLENGKETL
QRAEPPKTHV THHPLSDHEA TLRCWALGFY PAEITLTWQR DGEDQTQDTE LVETRPAGDG
TFQKWAAVVV PSGQEQRYTC HMQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLVVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAACSNS AQGSDESLIT CKA*

mutated AA sequence

MRVMAPRALL LLLSGGLALT ETWACECGVG REAASAERSE GPPGEPRREV GRAGLSPSSP
PGSHSMRYFD TAVSRPGRGE PRFISVGYVD DTQFVRFDSD AASPRGEPRA PWVEQEGPEY
WDRETQKYKR QAQTDRVSLR NLRGYYNQSE DGSHTLQRMS GCDLGPDGRL LRGYDQSAYD
GKDYIALNED LRSWTAADTA AQITQRKLEA ARAAEQLRAY LEGTCVEWLR RYLENGKETL
QRAEPPKTHV THHPLSDHEA TLRCWALGFY PAEITLTWQR DGEDQTQDTE LVETRPAGDG
TFQKWAAVVV PSGQEQRYTC HMQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLVVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAACSNS AQGSDESLIT CKA*

speed

1.26 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