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: ENST00000374409
Querying Taster for transcript #2: ENST00000003583
Querying Taster for transcript #3: ENST00000337248
Querying Taster for transcript #4: ENST00000440416
MT speed 0 s - this script 4.000422 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
STPG1	polymorphism_automatic	7.39629024693045e-10	simple_aae		affected		I105V	single base exchange	rs1142057		show file
STPG1	polymorphism_automatic	7.39629024693045e-10	simple_aae		affected		I58V	single base exchange	rs1142057		show file
STPG1	polymorphism_automatic	7.39629024693045e-10	simple_aae		affected		I105V	single base exchange	rs1142057		show file
STPG1	polymorphism_automatic	7.39629024693045e-10	simple_aae		affected		I58V	single base exchange	rs1142057		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999260371 (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)

chr1:24706292T>CN/A show variant in all transcripts IGV

HGNC symbol

STPG1

Ensembl transcript ID

ENST00000374409

Genbank transcript ID

NM_001199012

UniProt peptide

Q5TH74

alteration type

single base exchange

alteration region

CDS

DNA changes

c.313A>G
cDNA.568A>G
g.37133A>G

AA changes

I105V Score: 29 explain score(s)

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

105

frameshift

known variant

Reference ID: rs1142057

database	homozygous (C/C)	heterozygous	allele carriers
1000G	368	1095	1463
ExAC	7551	17665	25216

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.304	0
	-0.085	0
(flanking)	0.044	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
Acc marginally increased	37140	wt: 0.7861 / mu: 0.8396 (marginal change - not scored)	wt: ATTGGACACCATCATTTCTAAATACCCTGCAGCGAATGCAT mu: ATTGGACACCATCGTTTCTAAATACCCTGCAGCGAATGCAT	ctaa\|ATAC
Donor gained	37127	0.54	mu: TGGACACCATCGTTT	GACA\|ccat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

105

mutated

all conserved

105

Ptroglodytes

all identical

ENSPTRG00000000345

Mmulatta

all identical

ENSMMUG00000004464

105

Fcatus

all identical

ENSFCAG00000002066

105

Mmusculus

all identical

ENSMUSG00000028801

111

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000059171

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000031811

119

protein features

start (aa)	end (aa)	feature	details
105	105	CONFLICT	I -> V (in Ref. 2; AAH35061).	lost
163	163	CONFLICT	R -> I (in Ref. 2; AAH17650).	might get lost (downstream of altered splice site)
187	206	REPEAT	STPGR 2.	might get lost (downstream of altered splice site)
225	257	REPEAT	STPGR 3.	might get lost (downstream of altered splice site)
233	233	CONFLICT	P -> T (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)
267	282	REPEAT	STPGR 4.	might get lost (downstream of altered splice site)
306	316	REPEAT	STPGR 5.	might get lost (downstream of altered splice site)
332	332	CONFLICT	P -> R (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1005 / 1005

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

335 / 335

position of stopcodon in wt / mu cDNA

1260 / 1260

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

256 / 256

chromosome

strand

-1

last intron/exon boundary

1184

theoretical NMD boundary in CDS

878

length of CDS

1005

coding sequence (CDS) position

313

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

568

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

37133

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

24706292

original gDNA sequence snippet

GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG

altered gDNA sequence snippet

GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG

original cDNA sequence snippet

GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG

altered cDNA sequence snippet

GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG

wildtype AA sequence

MDNSAQKNER TGKHPRRASE VQKGFTAAYP TQSSIPFKSQ ASVIPESEKK GFNSQAKRFP
HKKNDIPGPG FYNVIHQSPV SNSVSLSKKG TCMFPSMCAR LDTIISKYPA ANAYTIPSDF
ISKRDFSNSC SSMFQLPSFM KALKFETPAP NYYNASVSCC KQRNNVCTRA GFMSKTQRGS
FAFADKGPPP GHYDINESLV KQSPNTLMSC FKSKTNRGLK LTSTGPGPGY YNPSDCTKVP
KKTLFPKNPI LNFSAQPSPL PPKPPFPGPG QYEIVDYLGP RKHFISSASF VSNTSRWTAA
PPQPGLPGPA TYKPELPGKQ SFLYNEDKKW IPVL*

mutated AA sequence

MDNSAQKNER TGKHPRRASE VQKGFTAAYP TQSSIPFKSQ ASVIPESEKK GFNSQAKRFP
HKKNDIPGPG FYNVIHQSPV SNSVSLSKKG TCMFPSMCAR LDTIVSKYPA ANAYTIPSDF
ISKRDFSNSC SSMFQLPSFM KALKFETPAP NYYNASVSCC KQRNNVCTRA GFMSKTQRGS
FAFADKGPPP GHYDINESLV KQSPNTLMSC FKSKTNRGLK LTSTGPGPGY YNPSDCTKVP
KKTLFPKNPI LNFSAQPSPL PPKPPFPGPG QYEIVDYLGP RKHFISSASF VSNTSRWTAA
PPQPGLPGPA TYKPELPGKQ SFLYNEDKKW IPVL*

speed

0.96 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: 0.999999999260371 (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)

chr1:24706292T>CN/A show variant in all transcripts IGV

HGNC symbol

STPG1

Ensembl transcript ID

ENST00000003583

Genbank transcript ID

NM_178122

UniProt peptide

Q5TH74

alteration type

single base exchange

alteration region

CDS

DNA changes

c.172A>G
cDNA.314A>G
g.37133A>G

AA changes

I58V Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs1142057

database	homozygous (C/C)	heterozygous	allele carriers
1000G	368	1095	1463
ExAC	7551	17665	25216

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.304	0
	-0.085	0
(flanking)	0.044	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
Acc marginally increased	37140	wt: 0.7861 / mu: 0.8396 (marginal change - not scored)	wt: ATTGGACACCATCATTTCTAAATACCCTGCAGCGAATGCAT mu: ATTGGACACCATCGTTTCTAAATACCCTGCAGCGAATGCAT	ctaa\|ATAC
Donor gained	37127	0.54	mu: TGGACACCATCGTTT	GACA\|ccat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000000345

Mmulatta

all identical

ENSMMUG00000004464

105

Fcatus

all identical

ENSFCAG00000002066

105

Mmusculus

all identical

ENSMUSG00000028801

111

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000059171

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000031811

119

protein features

start (aa)	end (aa)	feature	details
67	74	REPEAT	STPGR 1.	might get lost (downstream of altered splice site)
72	72	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
93	93	CONFLICT	M -> T (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)
105	105	CONFLICT	I -> V (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)
163	163	CONFLICT	R -> I (in Ref. 2; AAH17650).	might get lost (downstream of altered splice site)
187	206	REPEAT	STPGR 2.	might get lost (downstream of altered splice site)
225	257	REPEAT	STPGR 3.	might get lost (downstream of altered splice site)
233	233	CONFLICT	P -> T (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)
267	282	REPEAT	STPGR 4.	might get lost (downstream of altered splice site)
306	316	REPEAT	STPGR 5.	might get lost (downstream of altered splice site)
332	332	CONFLICT	P -> R (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

864 / 864

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

288 / 288

position of stopcodon in wt / mu cDNA

1006 / 1006

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

143 / 143

chromosome

strand

-1

last intron/exon boundary

930

theoretical NMD boundary in CDS

737

length of CDS

864

coding sequence (CDS) position

172

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

314

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

37133

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

24706292

original gDNA sequence snippet

GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG

altered gDNA sequence snippet

GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG

original cDNA sequence snippet

GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG

altered cDNA sequence snippet

GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG

wildtype AA sequence

MNALANIPDV PVKYRKNDIP GPGFYNVIHQ SPVSNSVSLS KKGTCMFPSM CARLDTIISK
YPAANAYTIP SDFISKRDFS NSCSSMFQLP SFMKALKFET PAPNYYNASV SCCKQRNNVC
TRAGFMSKTQ RGSFAFADKG PPPGHYDINE SLVKQSPNTL MSCFKSKTNR GLKLTSTGPG
PGYYNPSDCT KVPKKTLFPK NPILNFSAQP SPLPPKPPFP GPGQYEIVDY LGPRKHFISS
ASFVSNTSRW TAAPPQPGLP GPATYKPELP GKQSFLYNED KKWIPVL*

mutated AA sequence

MNALANIPDV PVKYRKNDIP GPGFYNVIHQ SPVSNSVSLS KKGTCMFPSM CARLDTIVSK
YPAANAYTIP SDFISKRDFS NSCSSMFQLP SFMKALKFET PAPNYYNASV SCCKQRNNVC
TRAGFMSKTQ RGSFAFADKG PPPGHYDINE SLVKQSPNTL MSCFKSKTNR GLKLTSTGPG
PGYYNPSDCT KVPKKTLFPK NPILNFSAQP SPLPPKPPFP GPGQYEIVDY LGPRKHFISS
ASFVSNTSRW TAAPPQPGLP GPATYKPELP GKQSFLYNED KKWIPVL*

speed

0.86 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999260371 (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)

chr1:24706292T>CN/A show variant in all transcripts IGV

HGNC symbol

STPG1

Ensembl transcript ID

ENST00000337248

Genbank transcript ID

NM_001199013

UniProt peptide

Q5TH74

alteration type

single base exchange

alteration region

CDS

DNA changes

c.313A>G
cDNA.448A>G
g.37133A>G

AA changes

I105V Score: 29 explain score(s)

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

105

frameshift

known variant

Reference ID: rs1142057

database	homozygous (C/C)	heterozygous	allele carriers
1000G	368	1095	1463
ExAC	7551	17665	25216

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.304	0
	-0.085	0
(flanking)	0.044	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
Acc marginally increased	37140	wt: 0.7861 / mu: 0.8396 (marginal change - not scored)	wt: ATTGGACACCATCATTTCTAAATACCCTGCAGCGAATGCAT mu: ATTGGACACCATCGTTTCTAAATACCCTGCAGCGAATGCAT	ctaa\|ATAC
Donor gained	37127	0.54	mu: TGGACACCATCGTTT	GACA\|ccat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

105

mutated

all conserved

105

Ptroglodytes

all identical

ENSPTRG00000000345

Mmulatta

all identical

ENSMMUG00000004464

105

Fcatus

all identical

ENSFCAG00000002066

105

Mmusculus

all identical

ENSMUSG00000028801

111

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000059171

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000031811

119

protein features

start (aa)	end (aa)	feature	details
105	105	CONFLICT	I -> V (in Ref. 2; AAH35061).	lost
163	163	CONFLICT	R -> I (in Ref. 2; AAH17650).	might get lost (downstream of altered splice site)
187	206	REPEAT	STPGR 2.	might get lost (downstream of altered splice site)
225	257	REPEAT	STPGR 3.	might get lost (downstream of altered splice site)
233	233	CONFLICT	P -> T (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)
267	282	REPEAT	STPGR 4.	might get lost (downstream of altered splice site)
306	316	REPEAT	STPGR 5.	might get lost (downstream of altered splice site)
332	332	CONFLICT	P -> R (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1005 / 1005

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

335 / 335

position of stopcodon in wt / mu cDNA

1140 / 1140

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

136 / 136

chromosome

strand

-1

last intron/exon boundary

1064

theoretical NMD boundary in CDS

878

length of CDS

1005

coding sequence (CDS) position

313

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

448

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

37133

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

24706292

original gDNA sequence snippet

GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG

altered gDNA sequence snippet

GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG

original cDNA sequence snippet

GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG

altered cDNA sequence snippet

GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG

wildtype AA sequence

mutated AA sequence

speed

0.96 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999260371 (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)

chr1:24706292T>CN/A show variant in all transcripts IGV

HGNC symbol

STPG1

Ensembl transcript ID

ENST00000440416

Genbank transcript ID

N/A

UniProt peptide

Q5TH74

alteration type

single base exchange

alteration region

CDS

DNA changes

c.172A>G
cDNA.265A>G
g.37133A>G

AA changes

I58V Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs1142057

database	homozygous (C/C)	heterozygous	allele carriers
1000G	368	1095	1463
ExAC	7551	17665	25216

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.304	0
	-0.085	0
(flanking)	0.044	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
Acc marginally increased	37140	wt: 0.7861 / mu: 0.8396 (marginal change - not scored)	wt: ATTGGACACCATCATTTCTAAATACCCTGCAGCGAATGCAT mu: ATTGGACACCATCGTTTCTAAATACCCTGCAGCGAATGCAT	ctaa\|ATAC
Donor gained	37127	0.54	mu: TGGACACCATCGTTT	GACA\|ccat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000000345

Mmulatta

all identical

ENSMMUG00000004464

105

Fcatus

all identical

ENSFCAG00000002066

105

Mmusculus

all identical

ENSMUSG00000028801

111

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000059171

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000031811

119

protein features

start (aa)	end (aa)	feature	details
67	74	REPEAT	STPGR 1.	might get lost (downstream of altered splice site)
72	72	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
93	93	CONFLICT	M -> T (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)
105	105	CONFLICT	I -> V (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)
163	163	CONFLICT	R -> I (in Ref. 2; AAH17650).	might get lost (downstream of altered splice site)
187	206	REPEAT	STPGR 2.	might get lost (downstream of altered splice site)
225	257	REPEAT	STPGR 3.	might get lost (downstream of altered splice site)
233	233	CONFLICT	P -> T (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)
267	282	REPEAT	STPGR 4.	might get lost (downstream of altered splice site)
306	316	REPEAT	STPGR 5.	might get lost (downstream of altered splice site)
332	332	CONFLICT	P -> R (in Ref. 2; AAH35061).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

864 / 864

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

288 / 288

position of stopcodon in wt / mu cDNA

957 / 957

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

94 / 94

chromosome

strand

-1

last intron/exon boundary

881

theoretical NMD boundary in CDS

737

length of CDS

864

coding sequence (CDS) position

172

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

265

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

37133

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

24706292

original gDNA sequence snippet

GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG

altered gDNA sequence snippet

GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG

original cDNA sequence snippet

GCGCCCGATTGGACACCATCATTTCTAAATACCCTGCAGCG

altered cDNA sequence snippet

GCGCCCGATTGGACACCATCGTTTCTAAATACCCTGCAGCG

wildtype AA sequence

mutated AA sequence

speed

0.91 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