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: ENST00000027335
Querying Taster for transcript #2: ENST00000441892
Querying Taster for transcript #3: ENST00000450165
MT speed 0 s - this script 3.819633 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CDH17	polymorphism_automatic	1.12996419998623e-08	simple_aae		affected		K115E	single base exchange	rs2243518		show file
CDH17	polymorphism_automatic	1.12996419998623e-08	simple_aae		affected		K115E	single base exchange	rs2243518		show file
CDH17	polymorphism_automatic	0.000559465599692999	simple_aae		affected		K115E	single base exchange	rs2243518		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999988700358 (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)

chr8:95188850T>CN/A show variant in all transcripts IGV

HGNC symbol

CDH17

Ensembl transcript ID

ENST00000027335

Genbank transcript ID

NM_001144663

UniProt peptide

Q12864

alteration type

single base exchange

alteration region

CDS

DNA changes

c.343A>G
cDNA.468A>G
g.40682A>G

AA changes

K115E Score: 56 explain score(s)

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

115

frameshift

known variant

Reference ID: rs2243518

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1636	746	2382
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.612	0.858
	0.541	0.857
(flanking)	0.051	0.86

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	40676	0.65	mu: CTATCACCATAGAAG	ATCA\|ccat
Donor gained	40681	0.97	mu: ACCATAGAAGTGAAG	CATA\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

115

mutated

all conserved

115

Ptroglodytes

all conserved

ENSPTRG00000020425

115

Mmulatta

all conserved

ENSMMUG00000020010

115

Fcatus

all conserved

ENSFCAG00000015508

115

Mmusculus

all conserved

ENSMUSG00000028217

114

Ggallus

not conserved

ENSGALG00000015947

114

Trubripes

not conserved

ENSTRUG00000010271

113

Drerio

all conserved

ENSDARG00000005112

113

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000014682

113

protein features

start (aa)	end (aa)	feature	details
23	787	TOPO_DOM	Extracellular (Potential).	lost
30	128	DOMAIN	Cadherin 1.	lost
129	244	DOMAIN	Cadherin 2.	might get lost (downstream of altered splice site)
149	149	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
184	184	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
245	340	DOMAIN	Cadherin 3.	might get lost (downstream of altered splice site)
250	250	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
341	449	DOMAIN	Cadherin 4.	might get lost (downstream of altered splice site)
419	419	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
450	566	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
456	456	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
546	546	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
548	548	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
567	667	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
587	587	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
668	777	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
722	722	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
788	808	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
809	832	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2499 / 2499

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

833 / 833

position of stopcodon in wt / mu cDNA

2624 / 2624

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

126 / 126

chromosome

strand

-1

last intron/exon boundary

2524

theoretical NMD boundary in CDS

2348

length of CDS

2499

coding sequence (CDS) position

343

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

468

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

40682

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

95188850

original gDNA sequence snippet

GTCCAGTCCCTATCACCATAAAAGTGAAGGACATCAACGAC

altered gDNA sequence snippet

GTCCAGTCCCTATCACCATAGAAGTGAAGGACATCAACGAC

original cDNA sequence snippet

GTCCAGTCCCTATCACCATAAAAGTGAAGGACATCAACGAC

altered cDNA sequence snippet

GTCCAGTCCCTATCACCATAGAAGTGAAGGACATCAACGAC

wildtype AA sequence

MILQAHLHSL CLLMLYLATG YGQEGKFSGP LKPMTFSIYE GQEPSQIIFQ FKANPPAVTF
ELTGETDNIF VIEREGLLYY NRALDRETRS THNLQVAALD ANGIIVEGPV PITIKVKDIN
DNRPTFLQSK YEGSVRQNSR PGKPFLYVNA TDLDDPATPN GQLYYQIVIQ LPMINNVMYF
QINNKTGAIS LTREGSQELN PAKNPSYNLV ISVKDMGGQS ENSFSDTTSV DIIVTENIWK
APKPVEMVEN STDPHPIKIT QVRWNDPGAQ YSLVDKEKLP RFPFSIDQEG DIYVTQPLDR
EEKDAYVFYA VAKDEYGKPL SYPLEIHVKV KDINDNPPTC PSPVTVFEVQ ENERLGNSIG
TLTAHDRDEE NTANSFLNYR IVEQTPKLPM DGLFLIQTYA GMLQLAKQSL KKQDTPQYNL
TIEVSDKDFK TLCFVQINVI DINDQIPIFE KSDYGNLTLA EDTNIGSTIL TIQATDADEP
FTGSSKILYH IIKGDSEGRL GVDTDPHTNT GYVIIKKPLD FETAAVSNIV FKAENPEPLV
FGVKYNASSF AKFTLIVTDV NEAPQFSQHV FQAKVSEDVA IGTKVGNVTA KDPEGLDISY
SLRGDTRGWL KIDHVTGEIF SVAPLDREAG SPYRVQVVAT EVGGSSLSSV SEFHLILMDV
NDNPPRLAKD YTGLFFCHPL SAPGSLIFEA TDDDQHLFRG PHFTFSLGSG SLQNDWEVSK
INGTHARLST RHTEFEEREY VVLIRINDGG RPPLEGIVSL PVTFCSCVEG SCFRPAGHQT
GIPTVGMAVG ILLTTLLVIG IILAVVFIRI KKDKGKDNVE SAQASEVKPL RS*

mutated AA sequence

MILQAHLHSL CLLMLYLATG YGQEGKFSGP LKPMTFSIYE GQEPSQIIFQ FKANPPAVTF
ELTGETDNIF VIEREGLLYY NRALDRETRS THNLQVAALD ANGIIVEGPV PITIEVKDIN
DNRPTFLQSK YEGSVRQNSR PGKPFLYVNA TDLDDPATPN GQLYYQIVIQ LPMINNVMYF
QINNKTGAIS LTREGSQELN PAKNPSYNLV ISVKDMGGQS ENSFSDTTSV DIIVTENIWK
APKPVEMVEN STDPHPIKIT QVRWNDPGAQ YSLVDKEKLP RFPFSIDQEG DIYVTQPLDR
EEKDAYVFYA VAKDEYGKPL SYPLEIHVKV KDINDNPPTC PSPVTVFEVQ ENERLGNSIG
TLTAHDRDEE NTANSFLNYR IVEQTPKLPM DGLFLIQTYA GMLQLAKQSL KKQDTPQYNL
TIEVSDKDFK TLCFVQINVI DINDQIPIFE KSDYGNLTLA EDTNIGSTIL TIQATDADEP
FTGSSKILYH IIKGDSEGRL GVDTDPHTNT GYVIIKKPLD FETAAVSNIV FKAENPEPLV
FGVKYNASSF AKFTLIVTDV NEAPQFSQHV FQAKVSEDVA IGTKVGNVTA KDPEGLDISY
SLRGDTRGWL KIDHVTGEIF SVAPLDREAG SPYRVQVVAT EVGGSSLSSV SEFHLILMDV
NDNPPRLAKD YTGLFFCHPL SAPGSLIFEA TDDDQHLFRG PHFTFSLGSG SLQNDWEVSK
INGTHARLST RHTEFEEREY VVLIRINDGG RPPLEGIVSL PVTFCSCVEG SCFRPAGHQT
GIPTVGMAVG ILLTTLLVIG IILAVVFIRI KKDKGKDNVE SAQASEVKPL RS*

speed

0.71 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: 0.999999988700358 (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)

chr8:95188850T>CN/A show variant in all transcripts IGV

HGNC symbol

CDH17

Ensembl transcript ID

ENST00000450165

Genbank transcript ID

N/A

UniProt peptide

Q12864

alteration type

single base exchange

alteration region

CDS

DNA changes

c.343A>G
cDNA.469A>G
g.40682A>G

AA changes

K115E Score: 56 explain score(s)

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

115

frameshift

known variant

Reference ID: rs2243518

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1636	746	2382
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.612	0.858
	0.541	0.857
(flanking)	0.051	0.86

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	40676	0.65	mu: CTATCACCATAGAAG	ATCA\|ccat
Donor gained	40681	0.97	mu: ACCATAGAAGTGAAG	CATA\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

115

mutated

all conserved

115

Ptroglodytes

all conserved

ENSPTRG00000020425

115

Mmulatta

all conserved

ENSMMUG00000020010

115

Fcatus

all conserved

ENSFCAG00000015508

115

Mmusculus

all conserved

ENSMUSG00000028217

114

Ggallus

not conserved

ENSGALG00000015947

114

Trubripes

not conserved

ENSTRUG00000010271

113

Drerio

all conserved

ENSDARG00000005112

113

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000014682

113

protein features

start (aa)	end (aa)	feature	details
23	787	TOPO_DOM	Extracellular (Potential).	lost
30	128	DOMAIN	Cadherin 1.	lost
129	244	DOMAIN	Cadherin 2.	might get lost (downstream of altered splice site)
149	149	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
184	184	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
245	340	DOMAIN	Cadherin 3.	might get lost (downstream of altered splice site)
250	250	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
341	449	DOMAIN	Cadherin 4.	might get lost (downstream of altered splice site)
419	419	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
450	566	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
456	456	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
546	546	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
548	548	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
567	667	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
587	587	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
668	777	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
722	722	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
788	808	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
809	832	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2499 / 2499

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

833 / 833

position of stopcodon in wt / mu cDNA

2625 / 2625

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

127 / 127

chromosome

strand

-1

last intron/exon boundary

2525

theoretical NMD boundary in CDS

2348

length of CDS

2499

coding sequence (CDS) position

343

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

469

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

40682

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

95188850

original gDNA sequence snippet

GTCCAGTCCCTATCACCATAAAAGTGAAGGACATCAACGAC

altered gDNA sequence snippet

GTCCAGTCCCTATCACCATAGAAGTGAAGGACATCAACGAC

original cDNA sequence snippet

GTCCAGTCCCTATCACCATAAAAGTGAAGGACATCAACGAC

altered cDNA sequence snippet

GTCCAGTCCCTATCACCATAGAAGTGAAGGACATCAACGAC

wildtype AA sequence

mutated AA sequence

speed

0.79 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999440534400307 (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)

chr8:95188850T>CN/A show variant in all transcripts IGV

HGNC symbol

CDH17

Ensembl transcript ID

ENST00000441892

Genbank transcript ID

N/A

UniProt peptide

Q12864

alteration type

single base exchange

alteration region

CDS

DNA changes

c.343A>G
cDNA.436A>G
g.40682A>G

AA changes

K115E Score: 56 explain score(s)

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

115

frameshift

known variant

Reference ID: rs2243518

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1636	746	2382
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.612	0.858
	0.541	0.857
(flanking)	0.051	0.86

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	40676	0.65	mu: CTATCACCATAGAAG	ATCA\|ccat
Donor gained	40681	0.97	mu: ACCATAGAAGTGAAG	CATA\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

115

mutated

all conserved

115

Ptroglodytes

all identical

ENSPTRG00000020425

329

Mmulatta

all identical

ENSMMUG00000020010

329

Fcatus

all conserved

ENSFCAG00000015508

115

Mmusculus

all identical

ENSMUSG00000028217

328

Ggallus

not conserved

ENSGALG00000015947

328

Trubripes

not conserved

ENSTRUG00000010271

380

Drerio

not conserved

ENSDARG00000005112

379

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000014682

321

protein features

start (aa)	end (aa)	feature	details
23	787	TOPO_DOM	Extracellular (Potential).	lost
30	128	DOMAIN	Cadherin 1.	lost
129	244	DOMAIN	Cadherin 2.	might get lost (downstream of altered splice site)
149	149	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
184	184	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
245	340	DOMAIN	Cadherin 3.	might get lost (downstream of altered splice site)
250	250	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
341	449	DOMAIN	Cadherin 4.	might get lost (downstream of altered splice site)
419	419	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
450	566	DOMAIN	Cadherin 5.	might get lost (downstream of altered splice site)
456	456	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
546	546	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
548	548	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
567	667	DOMAIN	Cadherin 6.	might get lost (downstream of altered splice site)
587	587	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
668	777	DOMAIN	Cadherin 7.	might get lost (downstream of altered splice site)
722	722	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
788	808	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
809	832	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1743 / 1743

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

581 / 581

position of stopcodon in wt / mu cDNA

1836 / 1836

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

1736

theoretical NMD boundary in CDS

1592

length of CDS

1743

coding sequence (CDS) position

343

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

436

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

40682

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

95188850

original gDNA sequence snippet

GTCCAGTCCCTATCACCATAAAAGTGAAGGACATCAACGAC

altered gDNA sequence snippet

GTCCAGTCCCTATCACCATAGAAGTGAAGGACATCAACGAC

original cDNA sequence snippet

GTCCAGTCCCTATCACCATAAAAGTGAAGGACATCAACGAC

altered cDNA sequence snippet

GTCCAGTCCCTATCACCATAGAAGTGAAGGACATCAACGAC

wildtype AA sequence

MILQAHLHSL CLLMLYLATG YGQEGKFSGP LKPMTFSIYE GQEPSQIIFQ FKANPPAVTF
ELTGETDNIF VIEREGLLYY NRALDRETRS THNLQVAALD ANGIIVEGPV PITIKVKDIN
DNRPTFLQSK YEGSVRQNSR PGNSIGTLTA HDRDEENTAN SFLNYRIVEQ TPKLPMDGLF
LIQTYAGMLQ LAKQSLKKQD TPQYNLTIEV SDKDFKTLCF VQINVIDIND QIPIFEKSDY
GNLTLAEDTN IGSTILTIQA TDADEPFTGS SKILYHIIKG DSEGRLGVDT DPHTNTGYVI
IKKPLDFETA AVSNIVFKAE NPEPLVFGVK YNASSFAKFT LIVTDVNEAP QFSQHVFQAK
VSEDVAIGTK VGNVTAKDPE GLDISYSLRG DTRGWLKIDH VTGEIFSVAP LDREAGSPYR
VQVVATEVGG SSLSSVSEFH LILMDVNDNP PRLAKDYTGL FFCHPLSAPG SLIFEATDDD
QHLFRGPHFT FSLGSGSLQN DWEVSKINGT HARLSTRHTE FEEREYVVLI RINDGGRPPL
EGIVSLPGII LAVVFIRIKK DKGKDNVESA QASEVKPLRS *

mutated AA sequence

MILQAHLHSL CLLMLYLATG YGQEGKFSGP LKPMTFSIYE GQEPSQIIFQ FKANPPAVTF
ELTGETDNIF VIEREGLLYY NRALDRETRS THNLQVAALD ANGIIVEGPV PITIEVKDIN
DNRPTFLQSK YEGSVRQNSR PGNSIGTLTA HDRDEENTAN SFLNYRIVEQ TPKLPMDGLF
LIQTYAGMLQ LAKQSLKKQD TPQYNLTIEV SDKDFKTLCF VQINVIDIND QIPIFEKSDY
GNLTLAEDTN IGSTILTIQA TDADEPFTGS SKILYHIIKG DSEGRLGVDT DPHTNTGYVI
IKKPLDFETA AVSNIVFKAE NPEPLVFGVK YNASSFAKFT LIVTDVNEAP QFSQHVFQAK
VSEDVAIGTK VGNVTAKDPE GLDISYSLRG DTRGWLKIDH VTGEIFSVAP LDREAGSPYR
VQVVATEVGG SSLSSVSEFH LILMDVNDNP PRLAKDYTGL FFCHPLSAPG SLIFEATDDD
QHLFRGPHFT FSLGSGSLQN DWEVSKINGT HARLSTRHTE FEEREYVVLI RINDGGRPPL
EGIVSLPGII LAVVFIRIKK DKGKDNVESA QASEVKPLRS *

speed

0.78 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