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: ENST00000375820
Querying Taster for transcript #2: ENST00000397198
MT speed 0 s - this script 4.021741 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COL4A1	disease_causing_automatic	0.999999999979162	simple_aae			0	G562E	single base exchange	rs121912857		show file
COL4A1	disease_causing_automatic	1	without_aae			0		single base exchange	rs121912857		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999979162 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM067659)
known disease mutation: rs17414 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:110839528C>TN/A show variant in all transcripts IGV

HGNC symbol

COL4A1

Ensembl transcript ID

ENST00000375820

Genbank transcript ID

NM_001845

UniProt peptide

P02462

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1685G>A
cDNA.1807G>A
g.119969G>A

AA changes

G562E Score: 98 explain score(s)

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

562

frameshift

known variant

Reference ID: rs121912857
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17414 (pathogenic for Brain small vessel disease 1 with or without ocular anomalies) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM067659)

known disease mutation at this position, please check HGMD for details (HGMD ID CM067659)
known disease mutation at this position, please check HGMD for details (HGMD ID CM067659)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.172	0.967
	5.335	1
(flanking)	5.335	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 marginally increased	119971	wt: 0.9970 / mu: 0.9984 (marginal change - not scored)	wt: CTGGAAGAGATGGCC mu: CTGAAAGAGATGGCC	GGAA\|gaga
Donor marginally increased	119966	wt: 0.8582 / mu: 0.8718 (marginal change - not scored)	wt: TTCTCCTGGAAGAGA mu: TTCTCCTGAAAGAGA	CTCC\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

562

mutated

not conserved

562

Ptroglodytes

all identical

ENSPTRG00000006031

500

Mmulatta

all identical

ENSMMUG00000022280

525

Fcatus

all identical

ENSFCAG00000014784

534

Mmusculus

all identical

ENSMUSG00000031502

562

Ggallus

all identical

ENSGALG00000016841

562

Trubripes

all identical

ENSTRUG00000006458

525

Drerio

all identical

ENSDARG00000055009

535

Dmelanogaster

no homologue

Celegans

all identical

F01G12.5

592

Xtropicalis

all identical

ENSXETG00000002637

559

protein features

start (aa)	end (aa)	feature	details
173	1440	REGION	Triple-helical region.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5010 / 5010

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

1670 / 1670

position of stopcodon in wt / mu cDNA

5132 / 5132

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

123 / 123

chromosome

strand

-1

last intron/exon boundary

5051

theoretical NMD boundary in CDS

4878

length of CDS

5010

coding sequence (CDS) position

1685

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

1807

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

119969

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

110839528

original gDNA sequence snippet

AGGGAGAGCGGGTTCTCCTGGAAGAGATGGCCATCCGGGTC

altered gDNA sequence snippet

AGGGAGAGCGGGTTCTCCTGAAAGAGATGGCCATCCGGGTC

original cDNA sequence snippet

AGGGAGAGCGGGTTCTCCTGGAAGAGATGGCCATCCGGGTC

altered cDNA sequence snippet

AGGGAGAGCGGGTTCTCCTGAAAGAGATGGCCATCCGGGTC

wildtype AA sequence

MGPRLSVWLL LLPAALLLHE EHSRAAAKGG CAGSGCGKCD CHGVKGQKGE RGLPGLQGVI
GFPGMQGPEG PQGPPGQKGD TGEPGLPGTK GTRGPPGASG YPGNPGLPGI PGQDGPPGPP
GIPGCNGTKG ERGPLGPPGL PGFAGNPGPP GLPGMKGDPG EILGHVPGML LKGERGFPGI
PGTPGPPGLP GLQGPVGPPG FTGPPGPPGP PGPPGEKGQM GLSFQGPKGD KGDQGVSGPP
GVPGQAQVQE KGDFATKGEK GQKGEPGFQG MPGVGEKGEP GKPGPRGKPG KDGDKGEKGS
PGFPGEPGYP GLIGRQGPQG EKGEAGPPGP PGIVIGTGPL GEKGERGYPG TPGPRGEPGP
KGFPGLPGQP GPPGLPVPGQ AGAPGFPGER GEKGDRGFPG TSLPGPSGRD GLPGPPGSPG
PPGQPGYTNG IVECQPGPPG DQGPPGIPGQ PGFIGEIGEK GQKGESCLIC DIDGYRGPPG
PQGPPGEIGF PGQPGAKGDR GLPGRDGVAG VPGPQGTPGL IGQPGAKGEP GEFYFDLRLK
GDKGDPGFPG QPGMTGRAGS PGRDGHPGLP GPKGSPGSVG LKGERGPPGG VGFPGSRGDT
GPPGPPGYGP AGPIGDKGQA GFPGGPGSPG LPGPKGEPGK IVPLPGPPGA EGLPGSPGFP
GPQGDRGFPG TPGRPGLPGE KGAVGQPGIG FPGPPGPKGV DGLPGDMGPP GTPGRPGFNG
LPGNPGVQGQ KGEPGVGLPG LKGLPGLPGI PGTPGEKGSI GVPGVPGEHG AIGPPGLQGI
RGEPGPPGLP GSVGSPGVPG IGPPGARGPP GGQGPPGLSG PPGIKGEKGF PGFPGLDMPG
PKGDKGAQGL PGITGQSGLP GLPGQQGAPG IPGFPGSKGE MGVMGTPGQP GSPGPVGAPG
LPGEKGDHGF PGSSGPRGDP GLKGDKGDVG LPGKPGSMDK VDMGSMKGQK GDQGEKGQIG
PIGEKGSRGD PGTPGVPGKD GQAGQPGQPG PKGDPGISGT PGAPGLPGPK GSVGGMGLPG
TPGEKGVPGI PGPQGSPGLP GDKGAKGEKG QAGPPGIGIP GLRGEKGDQG IAGFPGSPGE
KGEKGSIGIP GMPGSPGLKG SPGSVGYPGS PGLPGEKGDK GLPGLDGIPG VKGEAGLPGT
PGPTGPAGQK GEPGSDGIPG SAGEKGEPGL PGRGFPGFPG AKGDKGSKGE VGFPGLAGSP
GIPGSKGEQG FMGPPGPQGQ PGLPGSPGHA TEGPKGDRGP QGQPGLPGLP GPMGPPGLPG
IDGVKGDKGN PGWPGAPGVP GPKGDPGFQG MPGIGGSPGI TGSKGDMGPP GVPGFQGPKG
LPGLQGIKGD QGDQGVPGAK GLPGPPGPPG PYDIIKGEPG LPGPEGPPGL KGLQGLPGPK
GQQGVTGLVG IPGPPGIPGF DGAPGQKGEM GPAGPTGPRG FPGPPGPDGL PGSMGPPGTP
SVDHGFLVTR HSQTIDDPQC PSGTKILYHG YSLLYVQGNE RAHGQDLGTA GSCLRKFSTM
PFLFCNINNV CNFASRNDYS YWLSTPEPMP MSMAPITGEN IRPFISRCAV CEAPAMVMAV
HSQTIQIPPC PSGWSSLWIG YSFVMHTSAG AEGSGQALAS PGSCLEEFRS APFIECHGRG
TCNYYANAYS FWLATIERSE MFKKPTPSTL KAGELRTHVS RCQVCMRRT*

mutated AA sequence

MGPRLSVWLL LLPAALLLHE EHSRAAAKGG CAGSGCGKCD CHGVKGQKGE RGLPGLQGVI
GFPGMQGPEG PQGPPGQKGD TGEPGLPGTK GTRGPPGASG YPGNPGLPGI PGQDGPPGPP
GIPGCNGTKG ERGPLGPPGL PGFAGNPGPP GLPGMKGDPG EILGHVPGML LKGERGFPGI
PGTPGPPGLP GLQGPVGPPG FTGPPGPPGP PGPPGEKGQM GLSFQGPKGD KGDQGVSGPP
GVPGQAQVQE KGDFATKGEK GQKGEPGFQG MPGVGEKGEP GKPGPRGKPG KDGDKGEKGS
PGFPGEPGYP GLIGRQGPQG EKGEAGPPGP PGIVIGTGPL GEKGERGYPG TPGPRGEPGP
KGFPGLPGQP GPPGLPVPGQ AGAPGFPGER GEKGDRGFPG TSLPGPSGRD GLPGPPGSPG
PPGQPGYTNG IVECQPGPPG DQGPPGIPGQ PGFIGEIGEK GQKGESCLIC DIDGYRGPPG
PQGPPGEIGF PGQPGAKGDR GLPGRDGVAG VPGPQGTPGL IGQPGAKGEP GEFYFDLRLK
GDKGDPGFPG QPGMTGRAGS PERDGHPGLP GPKGSPGSVG LKGERGPPGG VGFPGSRGDT
GPPGPPGYGP AGPIGDKGQA GFPGGPGSPG LPGPKGEPGK IVPLPGPPGA EGLPGSPGFP
GPQGDRGFPG TPGRPGLPGE KGAVGQPGIG FPGPPGPKGV DGLPGDMGPP GTPGRPGFNG
LPGNPGVQGQ KGEPGVGLPG LKGLPGLPGI PGTPGEKGSI GVPGVPGEHG AIGPPGLQGI
RGEPGPPGLP GSVGSPGVPG IGPPGARGPP GGQGPPGLSG PPGIKGEKGF PGFPGLDMPG
PKGDKGAQGL PGITGQSGLP GLPGQQGAPG IPGFPGSKGE MGVMGTPGQP GSPGPVGAPG
LPGEKGDHGF PGSSGPRGDP GLKGDKGDVG LPGKPGSMDK VDMGSMKGQK GDQGEKGQIG
PIGEKGSRGD PGTPGVPGKD GQAGQPGQPG PKGDPGISGT PGAPGLPGPK GSVGGMGLPG
TPGEKGVPGI PGPQGSPGLP GDKGAKGEKG QAGPPGIGIP GLRGEKGDQG IAGFPGSPGE
KGEKGSIGIP GMPGSPGLKG SPGSVGYPGS PGLPGEKGDK GLPGLDGIPG VKGEAGLPGT
PGPTGPAGQK GEPGSDGIPG SAGEKGEPGL PGRGFPGFPG AKGDKGSKGE VGFPGLAGSP
GIPGSKGEQG FMGPPGPQGQ PGLPGSPGHA TEGPKGDRGP QGQPGLPGLP GPMGPPGLPG
IDGVKGDKGN PGWPGAPGVP GPKGDPGFQG MPGIGGSPGI TGSKGDMGPP GVPGFQGPKG
LPGLQGIKGD QGDQGVPGAK GLPGPPGPPG PYDIIKGEPG LPGPEGPPGL KGLQGLPGPK
GQQGVTGLVG IPGPPGIPGF DGAPGQKGEM GPAGPTGPRG FPGPPGPDGL PGSMGPPGTP
SVDHGFLVTR HSQTIDDPQC PSGTKILYHG YSLLYVQGNE RAHGQDLGTA GSCLRKFSTM
PFLFCNINNV CNFASRNDYS YWLSTPEPMP MSMAPITGEN IRPFISRCAV CEAPAMVMAV
HSQTIQIPPC PSGWSSLWIG YSFVMHTSAG AEGSGQALAS PGSCLEEFRS APFIECHGRG
TCNYYANAYS FWLATIERSE MFKKPTPSTL KAGELRTHVS RCQVCMRRT*

speed

1.34 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM067659)
known disease mutation: rs17414 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:110839528C>TN/A show variant in all transcripts IGV

HGNC symbol

COL4A1

Ensembl transcript ID

ENST00000397198

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.119969G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.172	0.967
	5.335	1
(flanking)	5.335	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 marginally increased	119971	wt: 0.9970 / mu: 0.9984 (marginal change - not scored)	wt: CTGGAAGAGATGGCC mu: CTGAAAGAGATGGCC	GGAA\|gaga
Donor marginally increased	119966	wt: 0.8582 / mu: 0.8718 (marginal change - not scored)	wt: TTCTCCTGGAAGAGA mu: TTCTCCTGAAAGAGA	CTCC\|tgga

distance from splice site

5077

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

123 / 123

chromosome

strand

-1

last intron/exon boundary

3998

theoretical NMD boundary in CDS

3825

length of CDS

3957

coding sequence (CDS) position

N/A

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

N/A

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

119969

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

110839528

original gDNA sequence snippet

AGGGAGAGCGGGTTCTCCTGGAAGAGATGGCCATCCGGGTC

altered gDNA sequence snippet

AGGGAGAGCGGGTTCTCCTGAAAGAGATGGCCATCCGGGTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MGPRLSVWLL LLPAALLLHE EHSRAAAKGG CAGSGCGKCD CHGVKGQKGE RGLPGLQGVI
GFPGMQGPEG PQGPPGQKGD TGEPGLPGTK GTRGPPGASG YPGNPGLPGI PGQDGPPGPP
GIPGCNGTKG ERGPLGPPGL PGFAGNPGPP GLPGMKGDPG EILGHVPGML LKGERGFPGI
PGTPGPPGLP GLQGPVGPPG FTGPPGPPGP PGPPGEKGQM GLSFQGPKGD KGDQGVSGPP
GVPGQAQVQE KGDFATKGEK GQKGEPGFQG MPGVGEKGEP GKPGPRGKPG KDGDKGEKGS
PGFPGEPGYP GLIGRQGPQG EKGEAGPPGP PGIVIGTGPL GEKGERGYPG TPGPRGEPGP
KGFPGLPGQP GPPGLPVPGQ AGAPGFPGER GEKGDRGFPG TSLPGPSGRD GLPGPPGSPG
PPGQPGYTNG IVECQPGPPG DQGPPGIPGQ PGFIGEIGEK GQKGESCLIC DIDGYRGPPG
PQGPPGEIGF PGQPGAKGLP GITGQSGLPG LPGQQGAPGI PGFPGSKGEM GVMGTPGQPG
SPGPVGAPGL PGEKGDHGFP GSSGPRGDPG LKGDKGDVGL PGKPGSMDKV DMGSMKGQKG
DQGEKGQIGP IGEKGSRGDP GTPGVPGKDG QAGQPGQPGP KGDPGISGTP GAPGLPGPKG
SVGGMGLPGT PGEKGVPGIP GPQGSPGLPG DKGAKGEKGQ AGPPGIGIPG LRGEKGDQGI
AGFPGSPGEK GEKGSIGIPG MPGSPGLKGS PGSVGYPGSP GLPGEKGDKG LPGLDGIPGV
KGEAGLPGTP GPTGPAGQKG EPGSDGIPGS AGEKGEPGLP GRGFPGFPGA KGDKGSKGEV
GFPGLAGSPG IPGSKGEQGF MGPPGPQGQP GLPGSPGHAT EGPKGDRGPQ GQPGLPGLPG
PMGPPGLPGI DGVKGDKGNP GWPGAPGVPG PKGDPGFQGM PGIGGSPGIT GSKGDMGPPG
VPGFQGPKGL PGLQGIKGDQ GDQGVPGAKG LPGPPGPPGP YDIIKGEPGL PGPEGPPGLK
GLQGLPGPKG QQGVTGLVGI PGPPGIPGFD GAPGQKGEMG PAGPTGPRGF PGPPGPDGLP
GSMGPPGTPS VDHGFLVTRH SQTIDDPQCP SGTKILYHGY SLLYVQGNER AHGQDLGTAG
SCLRKFSTMP FLFCNINNVC NFASRNDYSY WLSTPEPMPM SMAPITGENI RPFISRCAVC
EAPAMVMAVH SQTIQIPPCP SGWSSLWIGY SFVMHTSAGA EGSGQALASP GSCLEEFRSA
PFIECHGRGT CNYYANAYSF WLATIERSEM FKKPTPSTLK AGELRTHVSR CQVCMRRT*

mutated AA sequence

N/A

speed

0.73 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems