MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000310380
Querying Taster for transcript #2: ENST00000437101
Querying Taster for transcript #3: ENST00000429994
Querying Taster for transcript #4: ENST00000356740
Querying Taster for transcript #5: ENST00000355729
MT speed 0 s - this script 2.456035 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
XXYLT1	polymorphism_automatic	2.34035013590983e-13	simple_aae				R46P	single base exchange	rs60922537		show file
XXYLT1	polymorphism_automatic	2.47836221989317e-07	without_aae					single base exchange	rs60922537		show file
XXYLT1	polymorphism_automatic	2.47836221989317e-07	without_aae					single base exchange	rs60922537		show file
XXYLT1	polymorphism_automatic	2.47836221989317e-07	without_aae					single base exchange	rs60922537		show file
XXYLT1	polymorphism_automatic	2.47836221989317e-07	without_aae					single base exchange	rs60922537		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999766 (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)

chr3:194842785C>GN/A show variant in all transcripts IGV

HGNC symbol

XXYLT1

Ensembl transcript ID

ENST00000356740

Genbank transcript ID

N/A

UniProt peptide

Q8NBI6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.137G>C
cDNA.137G>C
g.149112G>C

AA changes

R46P Score: 103 explain score(s)

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

frameshift

known variant

Reference ID: rs60922537

database	homozygous (G/G)	heterozygous	allele carriers
1000G	351	998	1349
ExAC	353	2156	2509

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.515	0
	-1.501	0
(flanking)	1.011	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	149103	wt: 0.3095 / mu: 0.3389 (marginal change - not scored)	wt: GAATCAGTGGGCACG mu: GAATCAGTGGGCACC	ATCA\|gtgg

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

no alignment

ENSPTRG00000015761

n/a

Mmulatta

no alignment

ENSMMUG00000013091

n/a

Fcatus

all conserved

ENSFCAG00000012692

166

Mmusculus

no alignment

ENSMUSG00000047434

n/a

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000017377

n/a

Drerio

no alignment

ENSDARG00000088799

n/a

Dmelanogaster

no alignment

FBgn0034959

n/a

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000003454

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

564 / 564

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

188 / 188

position of stopcodon in wt / mu cDNA

564 / 564

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

168

theoretical NMD boundary in CDS

117

length of CDS

564

coding sequence (CDS) position

137

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

137

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

149112

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

194842785

original gDNA sequence snippet

GACACAGAATCAGTGGGCACGTTGGTCTTGGACTTCCCAGC

altered gDNA sequence snippet

GACACAGAATCAGTGGGCACCTTGGTCTTGGACTTCCCAGC

original cDNA sequence snippet

GACACAGAATCAGTGGGCACGTTGGTCTTGGACTTCCCAGC

altered cDNA sequence snippet

GACACAGAATCAGTGGGCACCTTGGTCTTGGACTTCCCAGC

wildtype AA sequence

MNGMSVLMKE TLKSSVTPSP YEETGERQPS VNWAVSPHQT QNQWARWSWT SQPLELHTFW
QFRHENPQTR VGGPPPEGLP GFNSGVMLLN LEAMRQSPLY SRLLEPAQVQ QLADKYHFRG
HLGDQDFFTM IGMEHPKLFH VLDCTWNRQL CTWWRDHGYS DVFEAYFRCE GHVKIYHGNC
NTPIPED*

mutated AA sequence

MNGMSVLMKE TLKSSVTPSP YEETGERQPS VNWAVSPHQT QNQWAPWSWT SQPLELHTFW
QFRHENPQTR VGGPPPEGLP GFNSGVMLLN LEAMRQSPLY SRLLEPAQVQ QLADKYHFRG
HLGDQDFFTM IGMEHPKLFH VLDCTWNRQL CTWWRDHGYS DVFEAYFRCE GHVKIYHGNC
NTPIPED*

speed

0.18 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: without_aae, prob: 0.999999752163778 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:194842785C>GN/A show variant in all transcripts IGV

HGNC symbol

XXYLT1

Ensembl transcript ID

ENST00000437101

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.149112G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs60922537

database	homozygous (G/G)	heterozygous	allele carriers
1000G	351	998	1349
ExAC	353	2156	2509

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.515	0
	-1.501	0
(flanking)	1.011	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	149103	wt: 0.3095 / mu: 0.3389 (marginal change - not scored)	wt: GAATCAGTGGGCACG mu: GAATCAGTGGGCACC	ATCA\|gtgg

distance from splice site

34393

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

463 / 463

chromosome

strand

-1

last intron/exon boundary

639

theoretical NMD boundary in CDS

126

length of CDS

573

coding sequence (CDS) position

N/A

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

N/A

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

149112

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

194842785

original gDNA sequence snippet

GACACAGAATCAGTGGGCACGTTGGTCTTGGACTTCCCAGC

altered gDNA sequence snippet

GACACAGAATCAGTGGGCACCTTGGTCTTGGACTTCCCAGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MWPPRCKDPG RQSAEILQII QLDLDLKFKT NIRELFEEFD SFLPGAIIGI AREMQPVYRH
TFWQFRHENP QTRVGGPPPE GLPGFNSGVM LLNLEAMRQS PLYSRLLEPA QVQQLADKYH
FRGHLGDQDF FTMIGMEHPK LFHVLDCTWN RQLCTWWRDH GYSDVFEAYF RCEGHVKIYH
GNCNTPIPED *

mutated AA sequence

N/A

speed

0.11 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999752163778 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:194842785C>GN/A show variant in all transcripts IGV

HGNC symbol

XXYLT1

Ensembl transcript ID

ENST00000429994

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.149112G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs60922537

database	homozygous (G/G)	heterozygous	allele carriers
1000G	351	998	1349
ExAC	353	2156	2509

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.515	0
	-1.501	0
(flanking)	1.011	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	149103	wt: 0.3095 / mu: 0.3389 (marginal change - not scored)	wt: GAATCAGTGGGCACG mu: GAATCAGTGGGCACC	ATCA\|gtgg

distance from splice site

34393

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

84 / 84

chromosome

strand

-1

last intron/exon boundary

431

theoretical NMD boundary in CDS

297

length of CDS

744

coding sequence (CDS) position

N/A

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

N/A

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

149112

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

194842785

original gDNA sequence snippet

GACACAGAATCAGTGGGCACGTTGGTCTTGGACTTCCCAGC

altered gDNA sequence snippet

GACACAGAATCAGTGGGCACCTTGGTCTTGGACTTCCCAGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVRCVPSAVI VCFLRPPQPG RTVIFHDVAV LTDKLFPIVE AMQKHFSAGL GTYYSDSIFF
LSVAMHQIMP KEILQIIQLD LDLKFKTNIR ELFEEFDSFL PGAIIGIARE MQPVYRHTFW
QFRHENPQTR VGGPPPEGLP GFNSGVMLLN LEAMRQSPLY SRLLEPAQVQ QLADKYHFRG
HLGDQDFFTM IGMEHPKLFH VLDCTWNRQL CTWWRDHGYS DVFEAYFRCE GHVKIYHGNC
NTPIPED*

mutated AA sequence

N/A

speed

0.15 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999752163778 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:194842785C>GN/A show variant in all transcripts IGV

HGNC symbol

XXYLT1

Ensembl transcript ID

ENST00000310380

Genbank transcript ID

NM_152531

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.149112G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs60922537

database	homozygous (G/G)	heterozygous	allele carriers
1000G	351	998	1349
ExAC	353	2156	2509

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.515	0
	-1.501	0
(flanking)	1.011	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	149103	wt: 0.3095 / mu: 0.3389 (marginal change - not scored)	wt: GAATCAGTGGGCACG mu: GAATCAGTGGGCACC	ATCA\|gtgg

distance from splice site

34393

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

110 / 110

chromosome

strand

-1

last intron/exon boundary

895

theoretical NMD boundary in CDS

735

length of CDS

1182

coding sequence (CDS) position

N/A

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

N/A

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

149112

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

194842785

original gDNA sequence snippet

GACACAGAATCAGTGGGCACGTTGGTCTTGGACTTCCCAGC

altered gDNA sequence snippet

GACACAGAATCAGTGGGCACCTTGGTCTTGGACTTCCCAGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MGLLRGGLPC ARAMARLGAV RSHYCALLLA AALAVCAFYY LGSGRETFSS ATKRLKEARA
GAPAAPSPPA LELARGSVAP APGAKAKSLE GGGAGPVDYH LLMMFTKAEH NAALQAKARV
ALRSLLRLAK FEAHEVLNLH FVSEEASREV AKGLLRELLP PAAGFKCKVI FHDVAVLTDK
LFPIVEAMQK HFSAGLGTYY SDSIFFLSVA MHQIMPKEIL QIIQLDLDLK FKTNIRELFE
EFDSFLPGAI IGIAREMQPV YRHTFWQFRH ENPQTRVGGP PPEGLPGFNS GVMLLNLEAM
RQSPLYSRLL EPAQVQQLAD KYHFRGHLGD QDFFTMIGME HPKLFHVLDC TWNRQLCTWW
RDHGYSDVFE AYFRCEGHVK IYHGNCNTPI PED*

mutated AA sequence

N/A

speed

0.15 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999752163778 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:194842785C>GN/A show variant in all transcripts IGV

HGNC symbol

XXYLT1

Ensembl transcript ID

ENST00000355729

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.149112G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs60922537

database	homozygous (G/G)	heterozygous	allele carriers
1000G	351	998	1349
ExAC	353	2156	2509

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.515	0
	-1.501	0
(flanking)	1.011	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	149103	wt: 0.3095 / mu: 0.3389 (marginal change - not scored)	wt: GAATCAGTGGGCACG mu: GAATCAGTGGGCACC	ATCA\|gtgg

distance from splice site

34393

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

177

theoretical NMD boundary in CDS

126

length of CDS

573

coding sequence (CDS) position

N/A

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

N/A

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

149112

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

194842785

original gDNA sequence snippet

GACACAGAATCAGTGGGCACGTTGGTCTTGGACTTCCCAGC

altered gDNA sequence snippet

GACACAGAATCAGTGGGCACCTTGGTCTTGGACTTCCCAGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.17 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

mutation t@sting

Prediction

polymorphism

Problems