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: ENST00000353479
Querying Taster for transcript #2: ENST00000369733
MT speed 0 s - this script 3.723085 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL17A1	disease_causing_automatic	0.999999973453807	simple_aae		affected	0	G633D	single base exchange	rs121912773		show file
COL17A1	disease_causing_automatic	0.999999999040174	simple_aae		affected	0	G633D	single base exchange	rs121912773		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999973453807 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM001970)
known disease mutation: rs17657 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:105812830C>TN/A show variant in all transcripts IGV

HGNC symbol

COL17A1

Ensembl transcript ID

ENST00000353479

Genbank transcript ID

NM_000494

UniProt peptide

Q9UMD9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1898G>A
cDNA.2189G>A
g.32931G>A

AA changes

G633D Score: 94 explain score(s)

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

633

frameshift

known variant

Reference ID: rs121912773
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17657 (pathogenic for Junctional epidermolysis bullosa, non-Herlitz type) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001970)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001970)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001970)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.174	0.999
	4.906	1
(flanking)	4.906	1

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 increased	32927	wt: 0.41 / mu: 0.97	wt: GACCTCGTGGTGAGG mu: GACCTCGTGATGAGG	CCTC\|gtgg
Donor marginally increased	32929	wt: 0.8614 / mu: 0.9373 (marginal change - not scored)	wt: CCTCGTGGTGAGGCA mu: CCTCGTGATGAGGCA	TCGT\|ggtg
Donor increased	32934	wt: 0.86 / mu: 0.95	wt: TGGTGAGGCAGGGCC mu: TGATGAGGCAGGGCC	GTGA\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

633

mutated

not conserved

633

Ptroglodytes

all identical

ENSPTRG00000002921

633

Mmulatta

all identical

ENSMMUG00000015325

631

Fcatus

all identical

ENSFCAG00000004299

633

Mmusculus

not conserved

ENSMUSG00000025064

624

Ggallus

all identical

ENSGALG00000008323

628

Trubripes

no homologue

Drerio

all identical

ENSDARG00000069415

706

Dmelanogaster

all identical

FBgn0035612

325

GGASGKPVY

RIST

Celegans

no alignment

F33A8.9

n/a

Xtropicalis

all identical

ENSXETG00000033563

638

protein features

start (aa)	end (aa)	feature	details
489	1497	TOPO_DOM	Extracellular (Potential).	lost
567	1482	REGION	Triple-helical region.	lost
856	856	CONFLICT	Q -> P (in Ref. 5; AAA51839).	might get lost (downstream of altered splice site)
905	905	CONFLICT	S -> F (in Ref. 1; AAA35605 and 2; AAB51499).	might get lost (downstream of altered splice site)
1421	1421	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1483	1497	REGION	Nonhelical region (NC1).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4494 / 4494

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

1498 / 1498

position of stopcodon in wt / mu cDNA

4785 / 4785

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

292 / 292

chromosome

strand

-1

last intron/exon boundary

4730

theoretical NMD boundary in CDS

4388

length of CDS

4494

coding sequence (CDS) position

1898

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

2189

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

32931

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

105812830

original gDNA sequence snippet

AGGCCCCATGGGACCTCGTGGTGAGGCAGGGCCTCCTGGAT

altered gDNA sequence snippet

AGGCCCCATGGGACCTCGTGATGAGGCAGGGCCTCCTGGAT

original cDNA sequence snippet

AGGCCCCATGGGACCTCGTGGTGAGGCAGGGCCTCCTGGAT

altered cDNA sequence snippet

AGGCCCCATGGGACCTCGTGATGAGGCAGGGCCTCCTGGAT

wildtype AA sequence

MDVTKKNKRD GTEVTERIVT ETVTTRLTSL PPKGGTSNGY AKTASLGGGS RLEKQSLTHG
SSGYINSTGS TRGHASTSSY RRAHSPASTL PNSPGSTFER KTHVTRHAYE GSSSGNSSPE
YPRKEFASSS TRGRSQTRES EIRVRLQSAS PSTRWTELDD VKRLLKGSRS ASVSPTRNSS
NTLPIPKKGT VETKIVTASS QSVSGTYDAT ILDANLPSHV WSSTLPAGSS MGTYHNNMTT
QSSSLLNTNA YSAGSVFGVP NNMASCSPTL HPGLSTSSSV FGMQNNLAPS LTTLSHGTTT
TSTAYGVKKN MPQSPAAVNT GVSTSAACTT SVQSDDLLHK DCKFLILEKD NTPAKKEMEL
LIMTKDSGKV FTASPASIAA TSFSEDTLKK EKQAAYNADS GLKAEANGDL KTVSTKGKTT
TADIHSYGSS GGGGSGGGGG VGGAGGGPWG PAPAWCPCGS CCSWWKWLLG LLLTWLLLLG
LLFGLIALAE EVRKLKARVD ELERIRRSIL PYGDSMDRIE KDRLQGMAPA AGADLDKIGL
HSDSQEELWM FVRKKLMMEQ ENGNLRGSPG PKGDMGSPGP KGDRGFPGTP GIPGPLGHPG
PQGPKGQKGS VGDPGMEGPM GQRGREGPMG PRGEAGPPGS GEKGERGAAG EPGPHGPPGV
PGSVGPKGSS GSPGPQGPPG PVGLQGLRGE VGLPGVKGDK GPMGPPGPKG DQGEKGPRGL
TGEPGMRGLP GAVGEPGAKG AMGPAGPDGH QGPRGEQGLT GMPGIRGPPG PSGDPGKPGL
TGPQGPQGLP GTPGRPGIKG EPGAPGKIVT SEGSSMLTVP GPPGPPGAMG PPGPPGAPGP
AGPAGLPGHQ EVLNLQGPPG PPGPRGPPGP SIPGPPGPRG PPGEGLPGPP GPPGSFLSNS
ETFLSGPPGP PGPPGPKGDQ GPPGPRGHQG EQGLPGFSTS GSSSFGLNLQ GPPGPPGPQG
PKGDKGDPGV PGALGIPSGP SEGGSSSTMY VSGPPGPPGP PGPPGSISSS GQEIQQYISE
YMQSDSIRSY LSGVQGPPGP PGPPGPVTTI TGETFDYSEL ASHVVSYLRT SGYGVSLFSS
SISSEDILAV LQRDDVRQYL RQYLMGPRGP PGPPGASGDG SLLSLDYAEL SSRILSYMSS
SGISIGLPGP PGPPGLPGTS YEELLSLLRG SEFRGIVGPP GPPGPPGIPG NVWSSISVED
LSSYLHTAGL SFIPGPPGPP GPPGPRGPPG VSGALATYAA ENSDSFRSEL ISYLTSPDVR
SFIVGPPGPP GPQGPPGDSR LLSTDASHSR GSSSSSHSSS VRRGSSYSSS MSTGGGGAGS
LGAGGAFGEA AGDRGPYGTD IGPGGGYGAA AEGGMYAGNG GLLGADFAGD LDYNELAVRV
SESMQRQGLL QGMAYTVQGP PGQPGPQGPP GISKVFSAYS NVTADLMDFF QTYGAIQGPP
GQKGEMGTPG PKGDRGPAGP PGHPGPPGPR GHKGEKGDKG DQVYAGRRRR RSIAVKP*

mutated AA sequence

MDVTKKNKRD GTEVTERIVT ETVTTRLTSL PPKGGTSNGY AKTASLGGGS RLEKQSLTHG
SSGYINSTGS TRGHASTSSY RRAHSPASTL PNSPGSTFER KTHVTRHAYE GSSSGNSSPE
YPRKEFASSS TRGRSQTRES EIRVRLQSAS PSTRWTELDD VKRLLKGSRS ASVSPTRNSS
NTLPIPKKGT VETKIVTASS QSVSGTYDAT ILDANLPSHV WSSTLPAGSS MGTYHNNMTT
QSSSLLNTNA YSAGSVFGVP NNMASCSPTL HPGLSTSSSV FGMQNNLAPS LTTLSHGTTT
TSTAYGVKKN MPQSPAAVNT GVSTSAACTT SVQSDDLLHK DCKFLILEKD NTPAKKEMEL
LIMTKDSGKV FTASPASIAA TSFSEDTLKK EKQAAYNADS GLKAEANGDL KTVSTKGKTT
TADIHSYGSS GGGGSGGGGG VGGAGGGPWG PAPAWCPCGS CCSWWKWLLG LLLTWLLLLG
LLFGLIALAE EVRKLKARVD ELERIRRSIL PYGDSMDRIE KDRLQGMAPA AGADLDKIGL
HSDSQEELWM FVRKKLMMEQ ENGNLRGSPG PKGDMGSPGP KGDRGFPGTP GIPGPLGHPG
PQGPKGQKGS VGDPGMEGPM GQRGREGPMG PRDEAGPPGS GEKGERGAAG EPGPHGPPGV
PGSVGPKGSS GSPGPQGPPG PVGLQGLRGE VGLPGVKGDK GPMGPPGPKG DQGEKGPRGL
TGEPGMRGLP GAVGEPGAKG AMGPAGPDGH QGPRGEQGLT GMPGIRGPPG PSGDPGKPGL
TGPQGPQGLP GTPGRPGIKG EPGAPGKIVT SEGSSMLTVP GPPGPPGAMG PPGPPGAPGP
AGPAGLPGHQ EVLNLQGPPG PPGPRGPPGP SIPGPPGPRG PPGEGLPGPP GPPGSFLSNS
ETFLSGPPGP PGPPGPKGDQ GPPGPRGHQG EQGLPGFSTS GSSSFGLNLQ GPPGPPGPQG
PKGDKGDPGV PGALGIPSGP SEGGSSSTMY VSGPPGPPGP PGPPGSISSS GQEIQQYISE
YMQSDSIRSY LSGVQGPPGP PGPPGPVTTI TGETFDYSEL ASHVVSYLRT SGYGVSLFSS
SISSEDILAV LQRDDVRQYL RQYLMGPRGP PGPPGASGDG SLLSLDYAEL SSRILSYMSS
SGISIGLPGP PGPPGLPGTS YEELLSLLRG SEFRGIVGPP GPPGPPGIPG NVWSSISVED
LSSYLHTAGL SFIPGPPGPP GPPGPRGPPG VSGALATYAA ENSDSFRSEL ISYLTSPDVR
SFIVGPPGPP GPQGPPGDSR LLSTDASHSR GSSSSSHSSS VRRGSSYSSS MSTGGGGAGS
LGAGGAFGEA AGDRGPYGTD IGPGGGYGAA AEGGMYAGNG GLLGADFAGD LDYNELAVRV
SESMQRQGLL QGMAYTVQGP PGQPGPQGPP GISKVFSAYS NVTADLMDFF QTYGAIQGPP
GQKGEMGTPG PKGDRGPAGP PGHPGPPGPR GHKGEKGDKG DQVYAGRRRR RSIAVKP*

speed

1.03 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

disease causing

Model: simple_aae, prob: 0.999999999040174 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM001970)
known disease mutation: rs17657 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:105812830C>TN/A show variant in all transcripts IGV

HGNC symbol

COL17A1

Ensembl transcript ID

ENST00000369733

Genbank transcript ID

N/A

UniProt peptide

Q9UMD9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1898G>A
cDNA.2189G>A
g.32931G>A

AA changes

G633D Score: 94 explain score(s)

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

633

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.174	0.999
	4.906	1
(flanking)	4.906	1

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 increased	32927	wt: 0.41 / mu: 0.97	wt: GACCTCGTGGTGAGG mu: GACCTCGTGATGAGG	CCTC\|gtgg
Donor marginally increased	32929	wt: 0.8614 / mu: 0.9373 (marginal change - not scored)	wt: CCTCGTGGTGAGGCA mu: CCTCGTGATGAGGCA	TCGT\|ggtg
Donor increased	32934	wt: 0.86 / mu: 0.95	wt: TGGTGAGGCAGGGCC mu: TGATGAGGCAGGGCC	GTGA\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

633

mutated

not conserved

633

Ptroglodytes

all identical

ENSPTRG00000002921

633

Mmulatta

all identical

ENSMMUG00000015325

631

Fcatus

all identical

ENSFCAG00000004299

633

Mmusculus

all identical

ENSMUSG00000025064

640

Ggallus

all identical

ENSGALG00000008323

628

Trubripes

no homologue

Drerio

all identical

ENSDARG00000069415

706

Dmelanogaster

all identical

FBgn0035612

266

Celegans

no alignment

F33A8.9

n/a

Xtropicalis

all identical

ENSXETG00000033563

638

protein features

start (aa)	end (aa)	feature	details
489	1497	TOPO_DOM	Extracellular (Potential).	lost
567	1482	REGION	Triple-helical region.	lost
856	856	CONFLICT	Q -> P (in Ref. 5; AAA51839).	might get lost (downstream of altered splice site)
905	905	CONFLICT	S -> F (in Ref. 1; AAA35605 and 2; AAB51499).	might get lost (downstream of altered splice site)
1421	1421	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1483	1497	REGION	Nonhelical region (NC1).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4248 / 4248

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

1416 / 1416

position of stopcodon in wt / mu cDNA

4539 / 4539

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

292 / 292

chromosome

strand

-1

last intron/exon boundary

4484

theoretical NMD boundary in CDS

4142

length of CDS

4248

coding sequence (CDS) position

1898

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

2189

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

32931

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

105812830

original gDNA sequence snippet

AGGCCCCATGGGACCTCGTGGTGAGGCAGGGCCTCCTGGAT

altered gDNA sequence snippet

AGGCCCCATGGGACCTCGTGATGAGGCAGGGCCTCCTGGAT

original cDNA sequence snippet

AGGCCCCATGGGACCTCGTGGTGAGGCAGGGCCTCCTGGAT

altered cDNA sequence snippet

AGGCCCCATGGGACCTCGTGATGAGGCAGGGCCTCCTGGAT

wildtype AA sequence

MDVTKKNKRD GTEVTERIVT ETVTTRLTSL PPKGGTSNGY AKTASLGGGS RLEKQSLTHG
SSGYINSTGS TRGHASTSSY RRAHSPASTL PNSPGSTFER KTHVTRHAYE GSSSGNSSPE
YPRKEFASSS TRGRSQTRES EIRVRLQSAS PSTRWTELDD VKRLLKGSRS ASVSPTRNSS
NTLPIPKKGT VETKIVTASS QSVSGTYDAT ILDANLPSHV WSSTLPAGSS MGTYHNNMTT
QSSSLLNTNA YSAGSVFGVP NNMASCSPTL HPGLSTSSSV FGMQNNLAPS LTTLSHGTTT
TSTAYGVKKN MPQSPAAVNT GVSTSAACTT SVQSDDLLHK DCKFLILEKD NTPAKKEMEL
LIMTKDSGKV FTASPASIAA TSFSEDTLKK EKQAAYNADS GLKAEANGDL KTVSTKGKTT
TADIHSYGSS GGGGSGGGGG VGGAGGGPWG PAPAWCPCGS CCSWWKWLLG LLLTWLLLLG
LLFGLIALAE EVRKLKARVD ELERIRRSIL PYGDSMDRIE KDRLQGMAPA AGADLDKIGL
HSDSQEELWM FVRKKLMMEQ ENGNLRGSPG PKGDMGSPGP KGDRGFPGTP GIPGPLGHPG
PQGPKGQKGS VGDPGMEGPM GQRGREGPMG PRGEAGPPGS GEKGERGAAG EPGPHGPPGV
PGSVGPKGSS GSPGPQGPPG PVGLQGLRGE VGLPGVKGDK GPMGPPGPKG DQGEKGPRGL
TGEPGMRGLP GAVGEPGAKG AMGPAGPDGH QGPRGEQGLT GMPGIRGPPG PSGDPGKPGL
TGPQGPQGLP GTPGRPGIKG EPGAPGKIVT SEGSSMLTVP GPPGPPGAMG PPGPPGAPGP
AGPAGLPGHQ EVLNLQGPPG PPGPRGPPGP SIPGPPGPRG PPGEGLPGPP GPPGSFLSNS
ETFLSGPPGP PGPPGPKGDQ GDPGVPGALG IPSGPSEGGS SSTMYVSGPP GPPGPPGPPG
SISSSGQEIQ QYISEYMQSD SIRSYLSGVQ GPPGPPGPPG PVTTITGETF DYSELASHVV
SYLRTSGYGV SLFSSSISSE DILAVLQRDD VRQYLRQYLM GPRGPPGPPG ASGDGSLLSL
DYAELSSRIL SYMSSSGISI GLPGPPGPPG LPGTSYEELL SLLRAAGLSF IPGPPGPPGP
PGPRGPPGVS GALATYAAEN SDSFRSELIS YLTSPDVRSF IVGPPGPPGP QGPPGDSRLL
STDASHSRGS SSSSHSSSVR RGSSYSSSMS TGGGGAGSLG AGGAFGEAAG DRGPYGTDIG
PGGGYGAAAE GGMYAGNGGL LGADFAGDLD YNELAVRVSE SMQRQGLLQG MAYTVQGPPG
QPGPQGPPGI SKVFSAYSNV TADLMDFFQT YGAIQGPPGQ KGEMGTPGPK GDRGPAGPPG
HPGPPGPRGH KGEKGDKGDQ VYAGRRRRRS IAVKP*

mutated AA sequence

MDVTKKNKRD GTEVTERIVT ETVTTRLTSL PPKGGTSNGY AKTASLGGGS RLEKQSLTHG
SSGYINSTGS TRGHASTSSY RRAHSPASTL PNSPGSTFER KTHVTRHAYE GSSSGNSSPE
YPRKEFASSS TRGRSQTRES EIRVRLQSAS PSTRWTELDD VKRLLKGSRS ASVSPTRNSS
NTLPIPKKGT VETKIVTASS QSVSGTYDAT ILDANLPSHV WSSTLPAGSS MGTYHNNMTT
QSSSLLNTNA YSAGSVFGVP NNMASCSPTL HPGLSTSSSV FGMQNNLAPS LTTLSHGTTT
TSTAYGVKKN MPQSPAAVNT GVSTSAACTT SVQSDDLLHK DCKFLILEKD NTPAKKEMEL
LIMTKDSGKV FTASPASIAA TSFSEDTLKK EKQAAYNADS GLKAEANGDL KTVSTKGKTT
TADIHSYGSS GGGGSGGGGG VGGAGGGPWG PAPAWCPCGS CCSWWKWLLG LLLTWLLLLG
LLFGLIALAE EVRKLKARVD ELERIRRSIL PYGDSMDRIE KDRLQGMAPA AGADLDKIGL
HSDSQEELWM FVRKKLMMEQ ENGNLRGSPG PKGDMGSPGP KGDRGFPGTP GIPGPLGHPG
PQGPKGQKGS VGDPGMEGPM GQRGREGPMG PRDEAGPPGS GEKGERGAAG EPGPHGPPGV
PGSVGPKGSS GSPGPQGPPG PVGLQGLRGE VGLPGVKGDK GPMGPPGPKG DQGEKGPRGL
TGEPGMRGLP GAVGEPGAKG AMGPAGPDGH QGPRGEQGLT GMPGIRGPPG PSGDPGKPGL
TGPQGPQGLP GTPGRPGIKG EPGAPGKIVT SEGSSMLTVP GPPGPPGAMG PPGPPGAPGP
AGPAGLPGHQ EVLNLQGPPG PPGPRGPPGP SIPGPPGPRG PPGEGLPGPP GPPGSFLSNS
ETFLSGPPGP PGPPGPKGDQ GDPGVPGALG IPSGPSEGGS SSTMYVSGPP GPPGPPGPPG
SISSSGQEIQ QYISEYMQSD SIRSYLSGVQ GPPGPPGPPG PVTTITGETF DYSELASHVV
SYLRTSGYGV SLFSSSISSE DILAVLQRDD VRQYLRQYLM GPRGPPGPPG ASGDGSLLSL
DYAELSSRIL SYMSSSGISI GLPGPPGPPG LPGTSYEELL SLLRAAGLSF IPGPPGPPGP
PGPRGPPGVS GALATYAAEN SDSFRSELIS YLTSPDVRSF IVGPPGPPGP QGPPGDSRLL
STDASHSRGS SSSSHSSSVR RGSSYSSSMS TGGGGAGSLG AGGAFGEAAG DRGPYGTDIG
PGGGYGAAAE GGMYAGNGGL LGADFAGDLD YNELAVRVSE SMQRQGLLQG MAYTVQGPPG
QPGPQGPPGI SKVFSAYSNV TADLMDFFQT YGAIQGPPGQ KGEMGTPGPK GDRGPAGPPG
HPGPPGPRGH KGEKGDKGDQ VYAGRRRRRS IAVKP*

speed

0.69 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems