MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000307078
Querying Taster for transcript #2: ENST00000375702
MT speed 0 s - this script 3.928502 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AXIN2	polymorphism_automatic	0.999193276637682	simple_aae		affected		P50S	single base exchange	rs2240308		show file
AXIN2	polymorphism_automatic	0.999193276637682	simple_aae		affected		P50S	single base exchange	rs2240308		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000806723362318307 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM066739)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:63554591G>AN/A show variant in all transcripts IGV

HGNC symbol

AXIN2

Ensembl transcript ID

ENST00000307078

Genbank transcript ID

NM_004655

UniProt peptide

Q9Y2T1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.148C>T
cDNA.462C>T
g.3175C>T

AA changes

P50S Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs2240308

database	homozygous (A/A)	heterozygous	allele carriers
1000G	376	939	1315
ExAC	14394	3979	18373

known disease mutation at this position, please check HGMD for details (HGMD ID CM066739)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.477	0.983
	0.711	0.976
(flanking)	1.262	0.97

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	3185	wt: 0.7301 / mu: 0.7438 (marginal change - not scored)	wt: CAAACCCATGCCTGTCTCTTCCAACACCAGGCGGAACGAAG mu: CAAACCCATGTCTGTCTCTTCCAACACCAGGCGGAACGAAG	cttc\|CAAC
Acc increased	3186	wt: 0.77 / mu: 0.85	wt: AAACCCATGCCTGTCTCTTCCAACACCAGGCGGAACGAAGA mu: AAACCCATGTCTGTCTCTTCCAACACCAGGCGGAACGAAGA	ttcc\|AACA
Acc increased	3177	wt: 0.25 / mu: 0.29	wt: CAGGTCACCAAACCCATGCCTGTCTCTTCCAACACCAGGCG mu: CAGGTCACCAAACCCATGTCTGTCTCTTCCAACACCAGGCG	gcct\|GTCT
Acc marginally increased	3184	wt: 0.6352 / mu: 0.6982 (marginal change - not scored)	wt: CCAAACCCATGCCTGTCTCTTCCAACACCAGGCGGAACGAA mu: CCAAACCCATGTCTGTCTCTTCCAACACCAGGCGGAACGAA	tctt\|CCAA
Donor marginally increased	3168	wt: 0.9798 / mu: 0.9895 (marginal change - not scored)	wt: ACCAAACCCATGCCT mu: ACCAAACCCATGTCT	CAAA\|ccca

distance from splice site

264

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000009554

Mmulatta

all identical

ENSMMUG00000016595

Fcatus

no alignment

ENSFCAG00000010038

n/a

Mmusculus

all identical

ENSMUSG00000000142

Ggallus

no alignment

ENSGALG00000004021

n/a

Trubripes

all identical

ENSTRUG00000005813

AQSR

SAAPPG

Drerio

all identical

ENSDARG00000014147

KTIMADLRC

Dmelanogaster

not conserved

FBgn0026597

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000013607

protein features

start (aa)	end (aa)	feature	details
37	62	CONFLICT	QPGVGKGQVTKPMSVSSNTRRNEDGL -> HHGGQGPGHQT HVCLFQHQAERRWV (in Ref. 2; AAF22799).	lost
81	200	DOMAIN	RGS.	might get lost (downstream of altered splice site)
327	413	REGION	Interaction with GSK3B (By similarity).	might get lost (downstream of altered splice site)
346	346	CONFLICT	Q -> R (in Ref. 2; AAF22799).	might get lost (downstream of altered splice site)
413	476	REGION	Interaction with beta-catenin (By similarity).	might get lost (downstream of altered splice site)
460	460	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
464	464	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
469	474	COMPBIAS	Poly-His.	might get lost (downstream of altered splice site)
572	636	CONFLICT	Missing (in Ref. 2; AAF22799).	might get lost (downstream of altered splice site)
630	630	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
639	639	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
640	640	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
687	687	CONFLICT	P -> S (in Ref. 2; AAF22799).	might get lost (downstream of altered splice site)
696	696	CONFLICT	Q -> H (in Ref. 2; AAF22799).	might get lost (downstream of altered splice site)
761	843	DOMAIN	DIX.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2532 / 2532

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

844 / 844

position of stopcodon in wt / mu cDNA

2846 / 2846

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

315 / 315

chromosome

strand

-1

last intron/exon boundary

2720

theoretical NMD boundary in CDS

2355

length of CDS

2532

coding sequence (CDS) position

148

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

462

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

3175

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

63554591

original gDNA sequence snippet

GCCAGGTCACCAAACCCATGCCTGTCTCTTCCAACACCAGG

altered gDNA sequence snippet

GCCAGGTCACCAAACCCATGTCTGTCTCTTCCAACACCAGG

original cDNA sequence snippet

GCCAGGTCACCAAACCCATGCCTGTCTCTTCCAACACCAGG

altered cDNA sequence snippet

GCCAGGTCACCAAACCCATGTCTGTCTCTTCCAACACCAGG

wildtype AA sequence

MSSAMLVTCL PDPSSSFRED APRPPVPGEE GETPPCQPGV GKGQVTKPMP VSSNTRRNED
GLGEPEGRAS PDSPLTRWTK SLHSLLGDQD GAYLFRTFLE REKCVDTLDF WFACNGFRQM
NLKDTKTLRV AKAIYKRYIE NNSIVSKQLK PATKTYIRDG IKKQQIDSIM FDQAQTEIQS
VMEENAYQMF LTSDIYLEYV RSGGENTAYM SNGGLGSLKV VCGYLPTLNE EEEWTCADFK
CKLSPTVVGL SSKTLRATAS VRSTETVDSG YRSFKRSDPV NPYHIGSGYV FAPATSANDS
EISSDALTDD SMSMTDSSVD GIPPYRVGSK KQLQREMHRS VKANGQVSLP HFPRTHRLPK
EMTPVEPATF AAELISRLEK LKLELESRHS LEERLQQIRE DEEREGSELT LNSREGAPTQ
HPLSLLPSGS YEEDPQTILD DHLSRVLKTP GCQSPGVGRY SPRSRSPDHH HHHHSQYHSL
LPPGGKLPPA AASPGACPLL GGKGFVTKQT TKHVHHHYIH HHAVPKTKEE IEAEATQRVH
CFCPGGSEYY CYSKCKSHSK APETMPSEQF GGSRGSTLPK RNGKGTEPGL ALPAREGGAP
GGAGALQLPR EEGDRSQDVW QWMLESERQS KPKPHSAQST KKAYPLESAR SSPGERASRH
HLWGGNSGHP RTTPRAHLFT QDPAMPPLTP PNTLAQLEEA CRRLAEVSKP PKQRCCVASQ
QRDRNHSATV QTGATPFSNP SLAPEDHKEP KKLAGVHALQ ASELVVTYFF CGEEIPYRRM
LKAQSLTLGH FKEQLSKKGN YRYYFKKASD EFACGAVFEE IWEDETVLPM YEGRILGKVE
RID*

mutated AA sequence

MSSAMLVTCL PDPSSSFRED APRPPVPGEE GETPPCQPGV GKGQVTKPMS VSSNTRRNED
GLGEPEGRAS PDSPLTRWTK SLHSLLGDQD GAYLFRTFLE REKCVDTLDF WFACNGFRQM
NLKDTKTLRV AKAIYKRYIE NNSIVSKQLK PATKTYIRDG IKKQQIDSIM FDQAQTEIQS
VMEENAYQMF LTSDIYLEYV RSGGENTAYM SNGGLGSLKV VCGYLPTLNE EEEWTCADFK
CKLSPTVVGL SSKTLRATAS VRSTETVDSG YRSFKRSDPV NPYHIGSGYV FAPATSANDS
EISSDALTDD SMSMTDSSVD GIPPYRVGSK KQLQREMHRS VKANGQVSLP HFPRTHRLPK
EMTPVEPATF AAELISRLEK LKLELESRHS LEERLQQIRE DEEREGSELT LNSREGAPTQ
HPLSLLPSGS YEEDPQTILD DHLSRVLKTP GCQSPGVGRY SPRSRSPDHH HHHHSQYHSL
LPPGGKLPPA AASPGACPLL GGKGFVTKQT TKHVHHHYIH HHAVPKTKEE IEAEATQRVH
CFCPGGSEYY CYSKCKSHSK APETMPSEQF GGSRGSTLPK RNGKGTEPGL ALPAREGGAP
GGAGALQLPR EEGDRSQDVW QWMLESERQS KPKPHSAQST KKAYPLESAR SSPGERASRH
HLWGGNSGHP RTTPRAHLFT QDPAMPPLTP PNTLAQLEEA CRRLAEVSKP PKQRCCVASQ
QRDRNHSATV QTGATPFSNP SLAPEDHKEP KKLAGVHALQ ASELVVTYFF CGEEIPYRRM
LKAQSLTLGH FKEQLSKKGN YRYYFKKASD EFACGAVFEE IWEDETVLPM YEGRILGKVE
RID*

speed

0.86 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: 0.000806723362318306 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM066739)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:63554591G>AN/A show variant in all transcripts IGV

HGNC symbol

AXIN2

Ensembl transcript ID

ENST00000375702

Genbank transcript ID

N/A

UniProt peptide

Q9Y2T1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.148C>T
cDNA.257C>T
g.3175C>T

AA changes

P50S Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs2240308

database	homozygous (A/A)	heterozygous	allele carriers
1000G	376	939	1315
ExAC	14394	3979	18373

known disease mutation at this position, please check HGMD for details (HGMD ID CM066739)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.477	0.983
	0.711	0.976
(flanking)	1.262	0.97

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	3185	wt: 0.7301 / mu: 0.7438 (marginal change - not scored)	wt: CAAACCCATGCCTGTCTCTTCCAACACCAGGCGGAACGAAG mu: CAAACCCATGTCTGTCTCTTCCAACACCAGGCGGAACGAAG	cttc\|CAAC
Acc increased	3186	wt: 0.77 / mu: 0.85	wt: AAACCCATGCCTGTCTCTTCCAACACCAGGCGGAACGAAGA mu: AAACCCATGTCTGTCTCTTCCAACACCAGGCGGAACGAAGA	ttcc\|AACA
Acc increased	3177	wt: 0.25 / mu: 0.29	wt: CAGGTCACCAAACCCATGCCTGTCTCTTCCAACACCAGGCG mu: CAGGTCACCAAACCCATGTCTGTCTCTTCCAACACCAGGCG	gcct\|GTCT
Acc marginally increased	3184	wt: 0.6352 / mu: 0.6982 (marginal change - not scored)	wt: CCAAACCCATGCCTGTCTCTTCCAACACCAGGCGGAACGAA mu: CCAAACCCATGTCTGTCTCTTCCAACACCAGGCGGAACGAA	tctt\|CCAA
Donor marginally increased	3168	wt: 0.9798 / mu: 0.9895 (marginal change - not scored)	wt: ACCAAACCCATGCCT mu: ACCAAACCCATGTCT	CAAA\|ccca

distance from splice site

257

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000009554

Mmulatta

all identical

ENSMMUG00000016595

Fcatus

no alignment

ENSFCAG00000010038

n/a

Mmusculus

all identical

ENSMUSG00000000142

Ggallus

no alignment

ENSGALG00000004021

n/a

Trubripes

all identical

ENSTRUG00000005813

AQSR

SAAPPG

Drerio

all identical

ENSDARG00000014147

KTIMADLRC

Dmelanogaster

not conserved

FBgn0026597

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000013607

protein features

start (aa)	end (aa)	feature	details
37	62	CONFLICT	QPGVGKGQVTKPMSVSSNTRRNEDGL -> HHGGQGPGHQT HVCLFQHQAERRWV (in Ref. 2; AAF22799).	lost
81	200	DOMAIN	RGS.	might get lost (downstream of altered splice site)
327	413	REGION	Interaction with GSK3B (By similarity).	might get lost (downstream of altered splice site)
346	346	CONFLICT	Q -> R (in Ref. 2; AAF22799).	might get lost (downstream of altered splice site)
413	476	REGION	Interaction with beta-catenin (By similarity).	might get lost (downstream of altered splice site)
460	460	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
464	464	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
469	474	COMPBIAS	Poly-His.	might get lost (downstream of altered splice site)
572	636	CONFLICT	Missing (in Ref. 2; AAF22799).	might get lost (downstream of altered splice site)
630	630	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
639	639	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
640	640	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
687	687	CONFLICT	P -> S (in Ref. 2; AAF22799).	might get lost (downstream of altered splice site)
696	696	CONFLICT	Q -> H (in Ref. 2; AAF22799).	might get lost (downstream of altered splice site)
761	843	DOMAIN	DIX.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2337 / 2337

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

779 / 779

position of stopcodon in wt / mu cDNA

2446 / 2446

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

2320

theoretical NMD boundary in CDS

2160

length of CDS

2337

coding sequence (CDS) position

148

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

257

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

3175

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

63554591

original gDNA sequence snippet

GCCAGGTCACCAAACCCATGCCTGTCTCTTCCAACACCAGG

altered gDNA sequence snippet

GCCAGGTCACCAAACCCATGTCTGTCTCTTCCAACACCAGG

original cDNA sequence snippet

GCCAGGTCACCAAACCCATGCCTGTCTCTTCCAACACCAGG

altered cDNA sequence snippet

GCCAGGTCACCAAACCCATGTCTGTCTCTTCCAACACCAGG

wildtype AA sequence

MSSAMLVTCL PDPSSSFRED APRPPVPGEE GETPPCQPGV GKGQVTKPMP VSSNTRRNED
GLGEPEGRAS PDSPLTRWTK SLHSLLGDQD GAYLFRTFLE REKCVDTLDF WFACNGFRQM
NLKDTKTLRV AKAIYKRYIE NNSIVSKQLK PATKTYIRDG IKKQQIDSIM FDQAQTEIQS
VMEENAYQMF LTSDIYLEYV RSGGENTAYM SNGGLGSLKV VCGYLPTLNE EEEWTCADFK
CKLSPTVVGL SSKTLRATAS VRSTETVDSG YRSFKRSDPV NPYHIGSGYV FAPATSANDS
EISSDALTDD SMSMTDSSVD GIPPYRVGSK KQLQREMHRS VKANGQVSLP HFPRTHRLPK
EMTPVEPATF AAELISRLEK LKLELESRHS LEERLQQIRE DEEREGSELT LNSREGAPTQ
HPLSLLPSGS YEEDPQTILD DHLSRVLKTP GCQSPGVGRY SPRSRSPDHH HHHHSQYHSL
LPPGGKLPPA AASPGACPLL GGKGFVTKQT TKHVHHHYIH HHAVPKTKEE IEAEATQRVH
CFCPGGSEYY CYSKCKSHSK APETMPSEQF GAQSTKKAYP LESARSSPGE RASRHHLWGG
NSGHPRTTPR AHLFTQDPAM PPLTPPNTLA QLEEACRRLA EVSKPPKQRC CVASQQRDRN
HSATVQTGAT PFSNPSLAPE DHKEPKKLAG VHALQASELV VTYFFCGEEI PYRRMLKAQS
LTLGHFKEQL SKKGNYRYYF KKASDEFACG AVFEEIWEDE TVLPMYEGRI LGKVERID*

mutated AA sequence

MSSAMLVTCL PDPSSSFRED APRPPVPGEE GETPPCQPGV GKGQVTKPMS VSSNTRRNED
GLGEPEGRAS PDSPLTRWTK SLHSLLGDQD GAYLFRTFLE REKCVDTLDF WFACNGFRQM
NLKDTKTLRV AKAIYKRYIE NNSIVSKQLK PATKTYIRDG IKKQQIDSIM FDQAQTEIQS
VMEENAYQMF LTSDIYLEYV RSGGENTAYM SNGGLGSLKV VCGYLPTLNE EEEWTCADFK
CKLSPTVVGL SSKTLRATAS VRSTETVDSG YRSFKRSDPV NPYHIGSGYV FAPATSANDS
EISSDALTDD SMSMTDSSVD GIPPYRVGSK KQLQREMHRS VKANGQVSLP HFPRTHRLPK
EMTPVEPATF AAELISRLEK LKLELESRHS LEERLQQIRE DEEREGSELT LNSREGAPTQ
HPLSLLPSGS YEEDPQTILD DHLSRVLKTP GCQSPGVGRY SPRSRSPDHH HHHHSQYHSL
LPPGGKLPPA AASPGACPLL GGKGFVTKQT TKHVHHHYIH HHAVPKTKEE IEAEATQRVH
CFCPGGSEYY CYSKCKSHSK APETMPSEQF GAQSTKKAYP LESARSSPGE RASRHHLWGG
NSGHPRTTPR AHLFTQDPAM PPLTPPNTLA QLEEACRRLA EVSKPPKQRC CVASQQRDRN
HSATVQTGAT PFSNPSLAPE DHKEPKKLAG VHALQASELV VTYFFCGEEI PYRRMLKAQS
LTLGHFKEQL SKKGNYRYYF KKASDEFACG AVFEEIWEDE TVLPMYEGRI LGKVERID*

speed

0.95 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems