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: ENST00000376228
Querying Taster for transcript #2: ENST00000383329
Querying Taster for transcript #3: ENST00000396254
Querying Taster for transcript #4: ENST00000539307
MT speed 2.92 s - this script 4.299359 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HLA-C	polymorphism_automatic	2.79987999451947e-09	simple_aae		affected		R121W	single base exchange	rs1131118		show file
HLA-C	polymorphism_automatic	2.79987999451947e-09	simple_aae		affected		R121W	single base exchange	rs1131118		show file
HLA-C	polymorphism_automatic	2.79987999451947e-09	simple_aae		affected		R121W	single base exchange	rs1131118		show file
HLA-C	polymorphism_automatic	2.79987999451947e-09	simple_aae		affected		R158W	single base exchange	rs1131118		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999720012 (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)

chr6:31239108T>AN/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.361A>T
cDNA.376A>T
g.800A>T

AA changes

R121W Score: 101 explain score(s)

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

121

frameshift

known variant

Reference ID: rs1131118

database	homozygous (A/A)	heterozygous	allele carriers
1000G	139	1064	1203
ExAC	3223	21902	25125

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
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
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.046	0
	-2.406	0.002
(flanking)	1.629	0.749

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	798	wt: 0.8089 / mu: 0.8378 (marginal change - not scored)	wt: CCTCCAGAGGATGTC mu: CCTCCAGTGGATGTC	TCCA\|gagg
Acc gained	798	0.36	mu: GCCAGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACC	tcca\|GTGG
Acc gained	802	0.42	mu: GGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTGGG	gtgg\|ATGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

121

mutated

not conserved

121

Ptroglodytes

not conserved

ENSPTRG00000041261

121

Mmulatta

not conserved

ENSMMUG00000029841

121

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
125	125	DISULFID	By similarity.	might get lost (downstream of altered splice site)
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	297	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	333	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
334	366	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

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

361

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

376

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

800

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

31239108

original gDNA sequence snippet

CAGGGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTG

altered gDNA sequence snippet

CAGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTG

original cDNA sequence snippet

ACGGGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTG

altered cDNA sequence snippet

ACGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTG

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 YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
WMSGCDLGPD 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

0.70 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: 0.99999999720012 (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)

chr6:31239108T>AN/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.361A>T
cDNA.376A>T
g.800A>T

AA changes

R121W Score: 101 explain score(s)

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

121

frameshift

known variant

Reference ID: rs1131118

database	homozygous (A/A)	heterozygous	allele carriers
1000G	139	1064	1203
ExAC	3223	21902	25125

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.046	0
	-2.406	0.002
(flanking)	1.629	0.749

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	798	wt: 0.8089 / mu: 0.8378 (marginal change - not scored)	wt: CCTCCAGAGGATGTC mu: CCTCCAGTGGATGTC	TCCA\|gagg
Acc gained	798	0.36	mu: GCCAGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACC	tcca\|GTGG
Acc gained	802	0.42	mu: GGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTGGG	gtgg\|ATGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

121

mutated

not conserved

121

Ptroglodytes

not conserved

ENSPTRG00000041261

121

Mmulatta

not conserved

ENSMMUG00000029841

121

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
125	125	DISULFID	By similarity.	might get lost (downstream of altered splice site)
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	297	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	333	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
334	366	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

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

361

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

376

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

800

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

31239108

original gDNA sequence snippet

CAGGGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTG

altered gDNA sequence snippet

CAGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTG

original cDNA sequence snippet

ACGGGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTG

altered cDNA sequence snippet

ACGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTG

wildtype AA sequence

mutated AA sequence

speed

0.91 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999720012 (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)

chr6:31239108T>AN/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.361A>T
cDNA.376A>T
g.800A>T

AA changes

R121W Score: 101 explain score(s)

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

121

frameshift

known variant

Reference ID: rs1131118

database	homozygous (A/A)	heterozygous	allele carriers
1000G	139	1064	1203
ExAC	3223	21902	25125

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.046	0
	-2.406	0.002
(flanking)	1.629	0.749

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	798	wt: 0.8089 / mu: 0.8378 (marginal change - not scored)	wt: CCTCCAGAGGATGTC mu: CCTCCAGTGGATGTC	TCCA\|gagg
Acc gained	798	0.36	mu: GCCAGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACC	tcca\|GTGG
Acc gained	802	0.42	mu: GGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTGGG	gtgg\|ATGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

121

mutated

not conserved

121

Ptroglodytes

not conserved

ENSPTRG00000041261

121

Mmulatta

not conserved

ENSMMUG00000029841

121

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
125	125	DISULFID	By similarity.	might get lost (downstream of altered splice site)
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	297	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	333	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
334	366	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

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

361

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

376

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

800

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

31239108

original gDNA sequence snippet

CAGGGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTG

altered gDNA sequence snippet

CAGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTG

original cDNA sequence snippet

ACGGGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTG

altered cDNA sequence snippet

ACGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTG

wildtype AA sequence

mutated AA sequence

speed

0.67 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999720012 (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)

chr6:31239108T>AN/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.472A>T
cDNA.472A>T
g.800A>T

AA changes

R158W Score: 101 explain score(s)

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

158

frameshift

known variant

Reference ID: rs1131118

database	homozygous (A/A)	heterozygous	allele carriers
1000G	139	1064	1203
ExAC	3223	21902	25125

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.046	0
	-2.406	0.002
(flanking)	1.629	0.749

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	798	wt: 0.8089 / mu: 0.8378 (marginal change - not scored)	wt: CCTCCAGAGGATGTC mu: CCTCCAGTGGATGTC	TCCA\|gagg
Acc gained	798	0.36	mu: GCCAGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACC	tcca\|GTGG
Acc gained	802	0.42	mu: GGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTGGG	gtgg\|ATGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

158

mutated

not conserved

158

Ptroglodytes

not conserved

ENSPTRG00000041261

121

Mmulatta

not conserved

ENSMMUG00000029841

117

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	297	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	333	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
334	366	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

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

472

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

472

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

800

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

31239108

original gDNA sequence snippet

CAGGGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTG

altered gDNA sequence snippet

CAGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTG

original cDNA sequence snippet

ACGGGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTG

altered cDNA sequence snippet

ACGGGTCTCACACCCTCCAGTGGATGTCTGGCTGCGACCTG

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 QAQADRVSLR NLRGYYNQSE DGSHTLQWMS 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

0.64 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