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: ENST00000532335
Querying Taster for transcript #2: ENST00000357183
Querying Taster for transcript #3: ENST00000367363
Querying Taster for transcript #4: ENST00000529948
MT speed 0 s - this script 2.955322 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RAET1E	polymorphism_automatic	2.92987856198579e-13	simple_aae				A141T	single base exchange	rs9383921		show file
RAET1E	polymorphism_automatic	2.92987856198579e-13	simple_aae				A141T	single base exchange	rs9383921		show file
RAET1E	polymorphism_automatic	2.92987856198579e-13	simple_aae				A105T	single base exchange	rs9383921		show file
RAET1E	polymorphism_automatic	2.92987856198579e-13	simple_aae				A141T	single base exchange	rs9383921		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999707 (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)

chr6:150210685C>TN/A show variant in all transcripts IGV

HGNC symbol

RAET1E

Ensembl transcript ID

ENST00000532335

Genbank transcript ID

NM_001243328

UniProt peptide

Q8TD07

alteration type

single base exchange

alteration region

CDS

DNA changes

c.421G>A
cDNA.768G>A
g.8554G>A

AA changes

A141T Score: 58 explain score(s)

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

141

frameshift

known variant

Reference ID: rs9383921

database	homozygous (T/T)	heterozygous	allele carriers
1000G	707	936	1643
ExAC	13026	6715	19741

regulatory features

Max, Transcription Factor, Max TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.071	0
	-0.295	0
(flanking)	-0.138	0.002

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	8557	wt: 0.9199 / mu: 0.9534 (marginal change - not scored)	wt: TCGCCACCAATGGAG mu: TCACCACCAATGGAG	GCCA\|ccaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

141

mutated

not conserved

141

Ptroglodytes

all identical

ENSPTRG00000022565

141

Mmulatta

not conserved

ENSMMUG00000005580

115

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
31	225	TOPO_DOM	Extracellular (Potential).	lost
117	207	REGION	MHC class I alpha-2 like.	lost
141	142	CONFLICT	AT -> TI (in Ref. 7; AAL76417).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

639 / 639

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

213 / 213

position of stopcodon in wt / mu cDNA

986 / 986

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

348 / 348

chromosome

strand

-1

last intron/exon boundary

970

theoretical NMD boundary in CDS

572

length of CDS

639

coding sequence (CDS) position

421

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

768

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

8554

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

150210685

original gDNA sequence snippet

CTGGTGCATCCTGGCAGTTCGCCACCAATGGAGAGAAATCC

altered gDNA sequence snippet

CTGGTGCATCCTGGCAGTTCACCACCAATGGAGAGAAATCC

original cDNA sequence snippet

CTGGTGCATCCTGGCAGTTCGCCACCAATGGAGAGAAATCC

altered cDNA sequence snippet

CTGGTGCATCCTGGCAGTTCACCACCAATGGAGAGAAATCC

wildtype AA sequence

MRRISLTSSP VRLLLFLLLL LIALEIMVGG HSLCFNFTIK SLSRPGQPWC EAQVFLNKNL
FLQYNSDNNM VKPLGLLGKK VYATSTWGEL TQTLGEVGRD LRMLLCDIKP QIKTSDPSTL
QVEMFCQREA ERCTGASWQF ATNGEKSLLF DAMNMTWTVI NHEASKIKET WKKDRGLEKY
FRKLSKGDCD HWLREFLGHW EAMPEPTGRR ST*

mutated AA sequence

MRRISLTSSP VRLLLFLLLL LIALEIMVGG HSLCFNFTIK SLSRPGQPWC EAQVFLNKNL
FLQYNSDNNM VKPLGLLGKK VYATSTWGEL TQTLGEVGRD LRMLLCDIKP QIKTSDPSTL
QVEMFCQREA ERCTGASWQF TTNGEKSLLF DAMNMTWTVI NHEASKIKET WKKDRGLEKY
FRKLSKGDCD HWLREFLGHW EAMPEPTGRR ST*

speed

0.31 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: 0.999999999999707 (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)

chr6:150210685C>TN/A show variant in all transcripts IGV

HGNC symbol

RAET1E

Ensembl transcript ID

ENST00000357183

Genbank transcript ID

NM_139165

UniProt peptide

Q8TD07

alteration type

single base exchange

alteration region

CDS

DNA changes

c.421G>A
cDNA.554G>A
g.8554G>A

AA changes

A141T Score: 58 explain score(s)

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

141

frameshift

known variant

Reference ID: rs9383921

database	homozygous (T/T)	heterozygous	allele carriers
1000G	707	936	1643
ExAC	13026	6715	19741

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.071	0
	-0.295	0
(flanking)	-0.138	0.002

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	8557	wt: 0.9199 / mu: 0.9534 (marginal change - not scored)	wt: TCGCCACCAATGGAG mu: TCACCACCAATGGAG	GCCA\|ccaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

141

mutated

not conserved

141

Ptroglodytes

all identical

ENSPTRG00000022565

141

Mmulatta

not conserved

ENSMMUG00000005580

115

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
31	225	TOPO_DOM	Extracellular (Potential).	lost
117	207	REGION	MHC class I alpha-2 like.	lost
141	142	CONFLICT	AT -> TI (in Ref. 7; AAL76417).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

792 / 792

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

264 / 264

position of stopcodon in wt / mu cDNA

925 / 925

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

134 / 134

chromosome

strand

-1

last intron/exon boundary

756

theoretical NMD boundary in CDS

572

length of CDS

792

coding sequence (CDS) position

421

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

554

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

8554

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

150210685

original gDNA sequence snippet

CTGGTGCATCCTGGCAGTTCGCCACCAATGGAGAGAAATCC

altered gDNA sequence snippet

CTGGTGCATCCTGGCAGTTCACCACCAATGGAGAGAAATCC

original cDNA sequence snippet

CTGGTGCATCCTGGCAGTTCGCCACCAATGGAGAGAAATCC

altered cDNA sequence snippet

CTGGTGCATCCTGGCAGTTCACCACCAATGGAGAGAAATCC

wildtype AA sequence

mutated AA sequence

speed

0.31 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999707 (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)

chr6:150210685C>TN/A show variant in all transcripts IGV

HGNC symbol

RAET1E

Ensembl transcript ID

ENST00000367363

Genbank transcript ID

NM_001243325

UniProt peptide

Q8TD07

alteration type

single base exchange

alteration region

CDS

DNA changes

c.313G>A
cDNA.446G>A
g.8554G>A

AA changes

A105T Score: 58 explain score(s)

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

105

frameshift

known variant

Reference ID: rs9383921

database	homozygous (T/T)	heterozygous	allele carriers
1000G	707	936	1643
ExAC	13026	6715	19741

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.071	0
	-0.295	0
(flanking)	-0.138	0.002

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	8557	wt: 0.9199 / mu: 0.9534 (marginal change - not scored)	wt: TCGCCACCAATGGAG mu: TCACCACCAATGGAG	GCCA\|ccaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

105

mutated

not conserved

105

Ptroglodytes

all identical

ENSPTRG00000022565

141

Mmulatta

not conserved

ENSMMUG00000005580

115

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
31	116	REGION	MHC class I alpha-1 like.	lost
31	225	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

684 / 684

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

228 / 228

position of stopcodon in wt / mu cDNA

817 / 817

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

134 / 134

chromosome

strand

-1

last intron/exon boundary

648

theoretical NMD boundary in CDS

464

length of CDS

684

coding sequence (CDS) position

313

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

446

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

8554

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

150210685

original gDNA sequence snippet

CTGGTGCATCCTGGCAGTTCGCCACCAATGGAGAGAAATCC

altered gDNA sequence snippet

CTGGTGCATCCTGGCAGTTCACCACCAATGGAGAGAAATCC

original cDNA sequence snippet

CTGGTGCATCCTGGCAGTTCGCCACCAATGGAGAGAAATCC

altered cDNA sequence snippet

CTGGTGCATCCTGGCAGTTCACCACCAATGGAGAGAAATCC

wildtype AA sequence

MRRISLTSSP VRLLLFLLLL LIALEIMYNS DNNMVKPLGL LGKKVYATST WGELTQTLGE
VGRDLRMLLC DIKPQIKTSD PSTLQVEMFC QREAERCTGA SWQFATNGEK SLLFDAMNMT
WTVINHEASK IKETWKKDRG LEKYFRKLSK GDCDHWLREF LGHWEAMPEP TVSPVNASDI
HWSSSSLPDR WIILGAFILL VLMGIVLICV WWQNGEWQAG LWPLRTS*

mutated AA sequence

MRRISLTSSP VRLLLFLLLL LIALEIMYNS DNNMVKPLGL LGKKVYATST WGELTQTLGE
VGRDLRMLLC DIKPQIKTSD PSTLQVEMFC QREAERCTGA SWQFTTNGEK SLLFDAMNMT
WTVINHEASK IKETWKKDRG LEKYFRKLSK GDCDHWLREF LGHWEAMPEP TVSPVNASDI
HWSSSSLPDR WIILGAFILL VLMGIVLICV WWQNGEWQAG LWPLRTS*

speed

0.30 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999707 (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)

chr6:150210685C>TN/A show variant in all transcripts IGV

HGNC symbol

RAET1E

Ensembl transcript ID

ENST00000529948

Genbank transcript ID

NM_001243327

UniProt peptide

Q8TD07

alteration type

single base exchange

alteration region

CDS

DNA changes

c.421G>A
cDNA.421G>A
g.8554G>A

AA changes

A141T Score: 58 explain score(s)

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

141

frameshift

known variant

Reference ID: rs9383921

database	homozygous (T/T)	heterozygous	allele carriers
1000G	707	936	1643
ExAC	13026	6715	19741

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.071	0
	-0.295	0
(flanking)	-0.138	0.002

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	8557	wt: 0.9199 / mu: 0.9534 (marginal change - not scored)	wt: TCGCCACCAATGGAG mu: TCACCACCAATGGAG	GCCA\|ccaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

141

mutated

not conserved

141

Ptroglodytes

all identical

ENSPTRG00000022565

141

Mmulatta

not conserved

ENSMMUG00000005580

115

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
31	225	TOPO_DOM	Extracellular (Potential).	lost
117	207	REGION	MHC class I alpha-2 like.	lost
141	142	CONFLICT	AT -> TI (in Ref. 7; AAL76417).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

630 / 630

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

210 / 210

position of stopcodon in wt / mu cDNA

630 / 630

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

347

theoretical NMD boundary in CDS

296

length of CDS

630

coding sequence (CDS) position

421

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

421

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

8554

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

150210685

original gDNA sequence snippet

CTGGTGCATCCTGGCAGTTCGCCACCAATGGAGAGAAATCC

altered gDNA sequence snippet

CTGGTGCATCCTGGCAGTTCACCACCAATGGAGAGAAATCC

original cDNA sequence snippet

CTGGTGCATCCTGGCAGTTCGCCACCAATGGAGAGAAATCC

altered cDNA sequence snippet

CTGGTGCATCCTGGCAGTTCACCACCAATGGAGAGAAATCC

wildtype AA sequence

mutated AA sequence

speed

0.33 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