MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000380534
Querying Taster for transcript #2: ENST00000380530
Querying Taster for transcript #3: ENST00000542071
MT speed 0 s - this script 3.565003 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SAXO1	polymorphism_automatic	1.99840144432528e-14	simple_aae		affected		P63S	single base exchange	rs6475273		show file
SAXO1	polymorphism_automatic	1.99840144432528e-14	simple_aae		affected		P63S	single base exchange	rs6475273		show file
SAXO1	polymorphism_automatic	1.76076363200828e-06	without_aae		affected			single base exchange	rs6475273		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999998 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:18950787G>AN/A show variant in all transcripts IGV

HGNC symbol

SAXO1

Ensembl transcript ID

ENST00000380534

Genbank transcript ID

NM_153707

UniProt peptide

Q8IYX7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.187C>T
cDNA.467C>T
g.82465C>T

AA changes

P63S Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs6475273

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1470	867	2337
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.074	0
	-0.145	0.002
(flanking)	0.249	0.027

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 gained	82458	0.46	mu: TACCAGAAAGGGTCT	CCAG\|aaag

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

not conserved

ENSPTRG00000020796

337

Mmulatta

not conserved

ENSMMUG00000018394

Fcatus

no alignment

ENSFCAG00000004841

n/a

Mmusculus

not conserved

ENSMUSG00000028492

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1425 / 1425

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

475 / 475

position of stopcodon in wt / mu cDNA

1705 / 1705

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

281 / 281

chromosome

strand

-1

last intron/exon boundary

702

theoretical NMD boundary in CDS

371

length of CDS

1425

coding sequence (CDS) position

187

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

467

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

82465

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

18950787

original gDNA sequence snippet

GGCGGGAGTACCAGAAAGGGCCTATACCAATGGAAGGCCTG

altered gDNA sequence snippet

GGCGGGAGTACCAGAAAGGGTCTATACCAATGGAAGGCCTG

original cDNA sequence snippet

GGCGGGAGTACCAGAAAGGGCCTATACCAATGGAAGGCCTG

altered cDNA sequence snippet

GGCGGGAGTACCAGAAAGGGTCTATACCAATGGAAGGCCTG

wildtype AA sequence

MKTKCICELC SCGRHHCPHL PTKIYDKTEK PCLLSEYTEN YPFYHSYLPR ESFKPRREYQ
KGPIPMEGLT TSRRDFGPHK VAPVKVHQYD QFVPSEENMD LLTTYKKDYN PYPVCRVDPI
KPRDSKYPCS DKMECLPTYK ADYLPWNQPR REPLRLEHKY QPASVRFDNR TTHQDDYPIK
GLVKTISCKP LAMPKLCNIP LEDVTNYKMS YVAHPVEKRF VHEAEKFRPC EIPFESLTTQ
KQSYRGLMGE PAKSLKPLAR PPGLDMPFCN TTEFRDKYQA WPMPRMFSKA PITYVPPEDR
MDLLTTVQAH YTCPKGAPAQ SCRPALQIKK CGRFEGSSTT KDDYKQWSSM RTEPVKPVPQ
LDLPTEPLDC LTTTRAHYVP HLPINTKSCK PHWSGPRGNV PVESQTTYTI SFTPKEMGRC
LASYPEPPGY TFEEVDALGH RIYKPVSQAG SQQSSHLSVD DSENPNQREL EVLA*

mutated AA sequence

MKTKCICELC SCGRHHCPHL PTKIYDKTEK PCLLSEYTEN YPFYHSYLPR ESFKPRREYQ
KGSIPMEGLT TSRRDFGPHK VAPVKVHQYD QFVPSEENMD LLTTYKKDYN PYPVCRVDPI
KPRDSKYPCS DKMECLPTYK ADYLPWNQPR REPLRLEHKY QPASVRFDNR TTHQDDYPIK
GLVKTISCKP LAMPKLCNIP LEDVTNYKMS YVAHPVEKRF VHEAEKFRPC EIPFESLTTQ
KQSYRGLMGE PAKSLKPLAR PPGLDMPFCN TTEFRDKYQA WPMPRMFSKA PITYVPPEDR
MDLLTTVQAH YTCPKGAPAQ SCRPALQIKK CGRFEGSSTT KDDYKQWSSM RTEPVKPVPQ
LDLPTEPLDC LTTTRAHYVP HLPINTKSCK PHWSGPRGNV PVESQTTYTI SFTPKEMGRC
LASYPEPPGY TFEEVDALGH RIYKPVSQAG SQQSSHLSVD DSENPNQREL EVLA*

speed

0.81 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: 0.99999999999998 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:18950787G>AN/A show variant in all transcripts IGV

HGNC symbol

SAXO1

Ensembl transcript ID

ENST00000380530

Genbank transcript ID

N/A

UniProt peptide

Q8IYX7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.187C>T
cDNA.532C>T
g.82465C>T

AA changes

P63S Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs6475273

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1470	867	2337
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.074	0
	-0.145	0.002
(flanking)	0.249	0.027

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 gained	82458	0.46	mu: TACCAGAAAGGGTCT	CCAG\|aaag

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

not conserved

ENSPTRG00000020796

Mmulatta

not conserved

ENSMMUG00000018394

Fcatus

no alignment

ENSFCAG00000004841

n/a

Mmusculus

not conserved

ENSMUSG00000028492

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

222 / 222

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

74 / 74

position of stopcodon in wt / mu cDNA

567 / 567

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

346 / 346

chromosome

strand

-1

last intron/exon boundary

564

theoretical NMD boundary in CDS

168

length of CDS

222

coding sequence (CDS) position

187

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

532

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

82465

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

18950787

original gDNA sequence snippet

GGCGGGAGTACCAGAAAGGGCCTATACCAATGGAAGGCCTG

altered gDNA sequence snippet

GGCGGGAGTACCAGAAAGGGTCTATACCAATGGAAGGCCTG

original cDNA sequence snippet

GGCGGGAGTACCAGAAAGGGCCTATACCAATGGAAGGCCTG

altered cDNA sequence snippet

GGCGGGAGTACCAGAAAGGGTCTATACCAATGGAAGGCCTG

wildtype AA sequence

MKTKCICELC SCGRHHCPHL PTKIYDKTEK PCLLSEYTEN YPFYHSYLPR ESFKPRREYQ
KGPIPMEGLT TSS*

mutated AA sequence

MKTKCICELC SCGRHHCPHL PTKIYDKTEK PCLLSEYTEN YPFYHSYLPR ESFKPRREYQ
KGSIPMEGLT TSS*

speed

0.58 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999998239236368 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:18950787G>AN/A show variant in all transcripts IGV

HGNC symbol

SAXO1

Ensembl transcript ID

ENST00000542071

Genbank transcript ID

N/A

UniProt peptide

Q8IYX7

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.532C>T
g.82465C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6475273

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1470	867	2337
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.074	0
	-0.145	0.002
(flanking)	0.249	0.027

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -63) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	82458	0.46	mu: TACCAGAAAGGGTCT	CCAG\|aaag

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

no protein features affected

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

719 / 719

chromosome

strand

-1

last intron/exon boundary

564

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

849

coding sequence (CDS) position

N/A

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

532

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

82465

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

18950787

original gDNA sequence snippet

GGCGGGAGTACCAGAAAGGGCCTATACCAATGGAAGGCCTG

altered gDNA sequence snippet

GGCGGGAGTACCAGAAAGGGTCTATACCAATGGAAGGCCTG

original cDNA sequence snippet

GGCGGGAGTACCAGAAAGGGCCTATACCAATGGAAGGCCTG

altered cDNA sequence snippet

GGCGGGAGTACCAGAAAGGGTCTATACCAATGGAAGGCCTG

wildtype AA sequence

MPKLCNIPLE DVTNYKMSYV AHPVEKRFVH EAEKFRPCEI PFESLTTQKQ SYRGLMGEPA
KSLKPLARPP GLDMPFCNTT EFRDKYQAWP MPRMFSKAPI TYVPPEDRMD LLTTVQAHYT
CPKGAPAQSC RPALQIKKCG RFEGSSTTKD DYKQWSSMRT EPVKPVPQLD LPTEPLDCLT
TTRAHYVPHL PINTKSCKPH WSGPRGNVPV ESQTTYTISF TPKEMGRCLA SYPEPPGYTF
EEVDALGHRI YKPVSQAGSQ QSSHLSVDDS ENPNQRELEV LA*

mutated AA sequence

N/A

speed

0.69 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