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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000519595
Querying Taster for transcript #2: ENST00000518642
Querying Taster for transcript #3: ENST00000250173
MT speed 0 s - this script 4.158145 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LRRC6	polymorphism_automatic	1.19904086659517e-14	simple_aae				T232I	single base exchange	rs2293979		show file
LRRC6	polymorphism_automatic	1.19904086659517e-14	simple_aae				T232I	single base exchange	rs2293979		show file
LRRC6	polymorphism_automatic	1.19904086659517e-14	simple_aae				T232I	single base exchange	rs2293979		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999988 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:133637659G>AN/A show variant in all transcripts IGV

HGNC symbol

LRRC6

Ensembl transcript ID

ENST00000519595

Genbank transcript ID

N/A

UniProt peptide

Q86X45

alteration type

single base exchange

alteration region

CDS

DNA changes

c.695C>T
cDNA.794C>T
g.50180C>T

AA changes

T232I Score: 89 explain score(s)

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

232

frameshift

known variant

Reference ID: rs2293979

database	homozygous (A/A)	heterozygous	allele carriers
1000G	765	905	1670
ExAC	11899	8969	20868

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.126	0
	-3.07	0
(flanking)	0.032	0

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	50178	wt: 0.2886 / mu: 0.3306 (marginal change - not scored)	wt: CCAGACACAGAGGAA mu: CCAGACATAGAGGAA	AGAC\|acag
Donor marginally increased	50183	wt: 0.9289 / mu: 0.9319 (marginal change - not scored)	wt: CACAGAGGAACACAA mu: CATAGAGGAACACAA	CAGA\|ggaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

232

mutated

not conserved

232

Ptroglodytes

not conserved

ENSPTRG00000020595

232

Mmulatta

all identical

ENSMMUG00000015647

232

Fcatus

not conserved

ENSFCAG00000008520

233

Mmusculus

not conserved

ENSMUSG00000022375

232

TQE

Ggallus

not conserved

ENSGALG00000016244

232

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000053318

232

Dmelanogaster

not conserved

FBgn0014395

214

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000023039

232

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1401 / 1401

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

467 / 467

position of stopcodon in wt / mu cDNA

1500 / 1500

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

100 / 100

chromosome

strand

-1

last intron/exon boundary

1326

theoretical NMD boundary in CDS

1176

length of CDS

1401

coding sequence (CDS) position

695

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

794

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

50180

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

133637659

original gDNA sequence snippet

CCACCTACAGGCACCAGACACAGAGGAACACAACACAAAGA

altered gDNA sequence snippet

CCACCTACAGGCACCAGACATAGAGGAACACAACACAAAGA

original cDNA sequence snippet

CCACCTACAGGCACCAGACACAGAGGAACACAACACAAAGA

altered cDNA sequence snippet

CCACCTACAGGCACCAGACATAGAGGAACACAACACAAAGA

wildtype AA sequence

MGWITEDLIR RNAEHNDCVI FSLEELSLHQ QEIERLEHID KWCRDLKILY LQNNLIGKIE
NVSKLKKLEY LNLALNNIEK IENLEGCEEL AKLDLTVNFI GELSSIKNLQ HNIHLKELFL
MGNPCASFDH YREFVVATLP QLKWLDGKEI EPSERIKALQ DYSVIEPQIR EQEKDHCLKR
AKLKEEAQRK HQEEDKNEDK RSNAGFDGRW YTDINATLSS LESKDHLQAP DTEEHNTKKL
DNSEDDLEFW NKPCLFTPES RLETLRHMEK QRKKQEKLSE KKKKVKPPRT LITEDGKALN
VNEPKIDFSL KDNEKQIILD LAVYRYMDTS LIDVDVQPTY VRVMIKGKPF QLVLPAEVKP
DSSSAKRSQT TGHLVICMPK VGEVITGGQR AFKSMKTTSD RSREQTNTRS KHMEKLEVDP
SKHSFPDVTN IVQEKKHTPR RRPEPKIIPS EEDPTFEDNP EVPPLI*

mutated AA sequence

MGWITEDLIR RNAEHNDCVI FSLEELSLHQ QEIERLEHID KWCRDLKILY LQNNLIGKIE
NVSKLKKLEY LNLALNNIEK IENLEGCEEL AKLDLTVNFI GELSSIKNLQ HNIHLKELFL
MGNPCASFDH YREFVVATLP QLKWLDGKEI EPSERIKALQ DYSVIEPQIR EQEKDHCLKR
AKLKEEAQRK HQEEDKNEDK RSNAGFDGRW YTDINATLSS LESKDHLQAP DIEEHNTKKL
DNSEDDLEFW NKPCLFTPES RLETLRHMEK QRKKQEKLSE KKKKVKPPRT LITEDGKALN
VNEPKIDFSL KDNEKQIILD LAVYRYMDTS LIDVDVQPTY VRVMIKGKPF QLVLPAEVKP
DSSSAKRSQT TGHLVICMPK VGEVITGGQR AFKSMKTTSD RSREQTNTRS KHMEKLEVDP
SKHSFPDVTN IVQEKKHTPR RRPEPKIIPS EEDPTFEDNP EVPPLI*

speed

1.37 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: 0.999999999999988 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:133637659G>AN/A show variant in all transcripts IGV

HGNC symbol

LRRC6

Ensembl transcript ID

ENST00000518642

Genbank transcript ID

N/A

UniProt peptide

Q86X45

alteration type

single base exchange

alteration region

CDS

DNA changes

c.695C>T
cDNA.761C>T
g.50180C>T

AA changes

T232I Score: 89 explain score(s)

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

232

frameshift

known variant

Reference ID: rs2293979

database	homozygous (A/A)	heterozygous	allele carriers
1000G	765	905	1670
ExAC	11899	8969	20868

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.126	0
	-3.07	0
(flanking)	0.032	0

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	50178	wt: 0.2886 / mu: 0.3306 (marginal change - not scored)	wt: CCAGACACAGAGGAA mu: CCAGACATAGAGGAA	AGAC\|acag
Donor marginally increased	50183	wt: 0.9289 / mu: 0.9319 (marginal change - not scored)	wt: CACAGAGGAACACAA mu: CATAGAGGAACACAA	CAGA\|ggaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

232

mutated

not conserved

232

Ptroglodytes

not conserved

ENSPTRG00000020595

232

Mmulatta

all identical

ENSMMUG00000015647

232

Fcatus

not conserved

ENSFCAG00000008520

233

Mmusculus

not conserved

ENSMUSG00000022375

232

TQE

Ggallus

not conserved

ENSGALG00000016244

232

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000053318

232

Dmelanogaster

not conserved

FBgn0014395

214

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000023039

232

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1236 / 1236

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

412 / 412

position of stopcodon in wt / mu cDNA

1302 / 1302

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

67 / 67

chromosome

strand

-1

last intron/exon boundary

1393

theoretical NMD boundary in CDS

1276

length of CDS

1236

coding sequence (CDS) position

695

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

761

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

50180

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

133637659

original gDNA sequence snippet

CCACCTACAGGCACCAGACACAGAGGAACACAACACAAAGA

altered gDNA sequence snippet

CCACCTACAGGCACCAGACATAGAGGAACACAACACAAAGA

original cDNA sequence snippet

CCACCTACAGGCACCAGACACAGAGGAACACAACACAAAGA

altered cDNA sequence snippet

CCACCTACAGGCACCAGACATAGAGGAACACAACACAAAGA

wildtype AA sequence

MGWITEDLIR RNAEHNDCVI FSLEELSLHQ QEIERLEHID KWCRDLKILY LQNNLIGKIE
NVSKLKKLEY LNLALNNIEK IENLEGCEEL AKLDLTVNFI GELSSIKNLQ HNIHLKELFL
MGNPCASFDH YREFVVATLP QLKWLDGKEI EPSERIKALQ DYSVIEPQIR EQEKDHCLKR
AKLKEEAQRK HQEEDKNEDK RSNAGFDGRW YTDINATLSS LESKDHLQAP DTEEHNTKKL
DNSEDDLEFW NKPCLFTPES RLETLRHMEK QRKKQEKLSE KKKKVKPPRT LITEDGKALN
VNEPKIDFSL KDNEKQIILD LAVYRYMDTS LIDVDVQPTY VRVMIKGKLV LPAEVKPDSS
SAKRSQTTGH LVICMPKVGE VITGGQRAFK SMKTTSDRSR EQTNTSYSTG F*

mutated AA sequence

MGWITEDLIR RNAEHNDCVI FSLEELSLHQ QEIERLEHID KWCRDLKILY LQNNLIGKIE
NVSKLKKLEY LNLALNNIEK IENLEGCEEL AKLDLTVNFI GELSSIKNLQ HNIHLKELFL
MGNPCASFDH YREFVVATLP QLKWLDGKEI EPSERIKALQ DYSVIEPQIR EQEKDHCLKR
AKLKEEAQRK HQEEDKNEDK RSNAGFDGRW YTDINATLSS LESKDHLQAP DIEEHNTKKL
DNSEDDLEFW NKPCLFTPES RLETLRHMEK QRKKQEKLSE KKKKVKPPRT LITEDGKALN
VNEPKIDFSL KDNEKQIILD LAVYRYMDTS LIDVDVQPTY VRVMIKGKLV LPAEVKPDSS
SAKRSQTTGH LVICMPKVGE VITGGQRAFK SMKTTSDRSR EQTNTSYSTG F*

speed

0.89 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999988 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:133637659G>AN/A show variant in all transcripts IGV

HGNC symbol

LRRC6

Ensembl transcript ID

ENST00000250173

Genbank transcript ID

NM_012472

UniProt peptide

Q86X45

alteration type

single base exchange

alteration region

CDS

DNA changes

c.695C>T
cDNA.769C>T
g.50180C>T

AA changes

T232I Score: 89 explain score(s)

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

232

frameshift

known variant

Reference ID: rs2293979

database	homozygous (A/A)	heterozygous	allele carriers
1000G	765	905	1670
ExAC	11899	8969	20868

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.126	0
	-3.07	0
(flanking)	0.032	0

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	50178	wt: 0.2886 / mu: 0.3306 (marginal change - not scored)	wt: CCAGACACAGAGGAA mu: CCAGACATAGAGGAA	AGAC\|acag
Donor marginally increased	50183	wt: 0.9289 / mu: 0.9319 (marginal change - not scored)	wt: CACAGAGGAACACAA mu: CATAGAGGAACACAA	CAGA\|ggaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

232

mutated

not conserved

232

Ptroglodytes

not conserved

ENSPTRG00000020595

232

Mmulatta

all identical

ENSMMUG00000015647

232

Fcatus

not conserved

ENSFCAG00000008520

233

Mmusculus

not conserved

ENSMUSG00000022375

232

TQE

Ggallus

not conserved

ENSGALG00000016244

232

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000053318

232

Dmelanogaster

not conserved

FBgn0014395

214

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000023039

232

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1401 / 1401

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

467 / 467

position of stopcodon in wt / mu cDNA

1475 / 1475

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

75 / 75

chromosome

strand

-1

last intron/exon boundary

1301

theoretical NMD boundary in CDS

1176

length of CDS

1401

coding sequence (CDS) position

695

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

769

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

50180

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

133637659

original gDNA sequence snippet

CCACCTACAGGCACCAGACACAGAGGAACACAACACAAAGA

altered gDNA sequence snippet

CCACCTACAGGCACCAGACATAGAGGAACACAACACAAAGA

original cDNA sequence snippet

CCACCTACAGGCACCAGACACAGAGGAACACAACACAAAGA

altered cDNA sequence snippet

CCACCTACAGGCACCAGACATAGAGGAACACAACACAAAGA

wildtype AA sequence

mutated AA sequence

MGWITEDLIR RNAEHNDCVI FSLEELSLHQ QEIERLEHID KWCRDLKILY LQNNLIGKIE
NVSKLKKLEY LNLALNNIEK IENLEGCEEL AKLDLTVNFI GELSSIKNLQ HNIHLKELFL
MGNPCASFDH YREFVVATLP QLKWLDGKEI EPSERIKALQ DYSVIEPQIR EQEKDHCLKR
AKLKEEAQRK HQEEDKNEDK RSNAGFDGRW YTDINATLSS LESKDHLQAP DIEEHNTKKL
DNSEDDLEFW NKPCLFTPES RLETLRHMEK QRKKQEKLSE KKKKVKPPRT LITEDGKALN
VNEPKIDFSL KDNEKQIILD LAVYRYMDTS LIDVDVQPTY VRVMIKGKPF QLVLPAEVKP
DSSSAKRSQT TGHLVICMPK VGEVITGGQR AFKSMKTTSD RSREQTNTRS KHMEKLEVDP
SKHSFPDVTN IVQEKKHTPR RRPEPKIIPS EEDPTFEDNP EVPPLI*

speed

0.45 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems