Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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: ENST00000375820
Querying Taster for transcript #2: ENST00000397198
Querying Taster for transcript #3: ENST00000543140
MT speed 0 s - this script 2.48829 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
COL4A1polymorphism_automatic0.00291454932673496simple_aaeaffectedV7Lsingle base exchangers9515185show file
COL4A1polymorphism_automatic0.00291454932673496simple_aaeaffectedV7Lsingle base exchangers9515185show file
COL4A1polymorphism_automatic0.00291454932673496simple_aaeaffectedV7Lsingle base exchangers9515185show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.997085450673265 (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) chr13:110959356C>GN/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.19G>C
cDNA.141G>C
g.141G>C
AA changes V7L Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 7
frameshift no
known variant Reference ID: rs9515185
databasehomozygous (G/G)heterozygousallele carriers
1000G52010841604
ExAC125625193775
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7720.991
0.3150.972
(flanking)0.330.957
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased144wt: 0.57 / mu: 0.68wt: TGGGGCCCCGGCTCAGCGTCTGGCTGCTGCTGCTGCCCGCC
mu: TGGGGCCCCGGCTCAGCCTCTGGCTGCTGCTGCTGCCCGCC		 gtct|GGCT
Acc gained1520.37mu: CGGCTCAGCCTCTGGCTGCTGCTGCTGCCCGCCGCCCTTCT gctg|CTGC
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      7 MGPRLSVWLLLLPAALLLH
mutated  all conserved    7 MGPRLSLWLLLLPAALLLHEEH
Ptroglodytes  all identical  ENSPTRG00000006031  7 MGPRLSVWLLLLPAALLLHEEH
Mmulatta  no alignment  ENSMMUG00000022280  n/a
Fcatus  no alignment  ENSFCAG00000014784  n/a
Mmusculus  all identical  ENSMUSG00000031502  7 MGPRLSVWLLLLFAALLLHEER
Ggallus  no alignment  ENSGALG00000016841  n/a
Trubripes  no alignment  ENSTRUG00000006458  n/a
Drerio  no alignment  ENSDARG00000055009  n/a
Dmelanogaster  no homologue    
Celegans  all conserved  F01G12.5  13 LGPVLRLAILALLAVSYVQSQ-
Xtropicalis  no alignment  ENSXETG00000002637  n/a
protein features
start (aa)end (aa)featuredetails 
127SIGNALlost
28172PROPEPN-terminal propeptide (7S domain). /FTId=PRO_0000005748.might get lost (downstream of altered splice site)
126126CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
1731440REGIONTriple-helical region.might get lost (downstream of altered splice site)
237238CONFLICTSG -> KE (in Ref. 6; AA sequence).might get lost (downstream of altered splice site)
241241CONFLICTG -> K (in Ref. 6; AA sequence).might get lost (downstream of altered splice site)
319319CONFLICTQ -> A (in Ref. 4; CAA29075).might get lost (downstream of altered splice site)
719719CONFLICTN -> D (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
837837CONFLICTD -> Y (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
842842CONFLICTK -> P (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
896896CONFLICTV -> W (in Ref. 7; CAA68698).might get lost (downstream of altered splice site)
904904CONFLICTE -> Q (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
914914CONFLICTS -> K (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
998998CONFLICTS -> K (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
10101010CONFLICTK -> P (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
10121012CONFLICTS -> K (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
13581358CONFLICTE -> Q (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
14451669DOMAINCollagen IV NC1.might get lost (downstream of altered splice site)
14461451STRANDmight get lost (downstream of altered splice site)
14531456STRANDmight get lost (downstream of altered splice site)
14601460DISULFIDmight get lost (downstream of altered splice site)
14651478STRANDmight get lost (downstream of altered splice site)
14811484STRANDmight get lost (downstream of altered splice site)
14901490CONFLICTA -> T (in Ref. 17; ABE73157).might get lost (downstream of altered splice site)
14901492HELIXmight get lost (downstream of altered splice site)
14931493DISULFIDmight get lost (downstream of altered splice site)
14931496STRANDmight get lost (downstream of altered splice site)
15021505STRANDmight get lost (downstream of altered splice site)
15051505DISULFIDmight get lost (downstream of altered splice site)
15071507CONFLICTI -> T (in Ref. 17; ABE73157).might get lost (downstream of altered splice site)
15091514STRANDmight get lost (downstream of altered splice site)
15111511DISULFIDmight get lost (downstream of altered splice site)
15191519CONFLICTY -> C (in Ref. 17; ABE73157).might get lost (downstream of altered splice site)
15191524STRANDmight get lost (downstream of altered splice site)
15331533CROSSLNKS-Lysyl-methionine sulfilimine (Met-Lys) (interchain with K-1651).might get lost (downstream of altered splice site)
15381544HELIXmight get lost (downstream of altered splice site)
15471555STRANDmight get lost (downstream of altered splice site)
15481548DISULFIDmight get lost (downstream of altered splice site)
15511551DISULFIDmight get lost (downstream of altered splice site)
15571561STRANDmight get lost (downstream of altered splice site)
15631566STRANDmight get lost (downstream of altered splice site)
15701570CONFLICTC -> Y (in Ref. 16; AAM97359).might get lost (downstream of altered splice site)
15701570DISULFIDmight get lost (downstream of altered splice site)
15741587STRANDmight get lost (downstream of altered splice site)
15891591HELIXmight get lost (downstream of altered splice site)
15931595STRANDmight get lost (downstream of altered splice site)
16011603HELIXmight get lost (downstream of altered splice site)
16041604DISULFIDmight get lost (downstream of altered splice site)
16041607STRANDmight get lost (downstream of altered splice site)
16131617STRANDmight get lost (downstream of altered splice site)
16161616DISULFIDmight get lost (downstream of altered splice site)
16201623STRANDmight get lost (downstream of altered splice site)
16221622DISULFIDmight get lost (downstream of altered splice site)
16291634STRANDmight get lost (downstream of altered splice site)
16381640HELIXmight get lost (downstream of altered splice site)
16481651STRANDmight get lost (downstream of altered splice site)
16511651CROSSLNKS-Lysyl-methionine sulfilimine (Lys-Met) (interchain with M-1533).might get lost (downstream of altered splice site)
16551658HELIXmight get lost (downstream of altered splice site)
16611667STRANDmight get lost (downstream of altered splice site)
16621662DISULFIDmight get lost (downstream of altered splice site)
16651665DISULFIDmight get lost (downstream of altered splice site)
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 13
strand -1
last intron/exon boundary 5051
theoretical NMD boundary in CDS 4878
length of CDS 5010
coding sequence (CDS) position 19
cDNA position
(for ins/del: last normal base / first normal base)		 141
gDNA position
(for ins/del: last normal base / first normal base)		 141
chromosomal position
(for ins/del: last normal base / first normal base)		 110959356
original gDNA sequence snippet CCATGGGGCCCCGGCTCAGCGTCTGGCTGCTGCTGCTGCCC
altered gDNA sequence snippet CCATGGGGCCCCGGCTCAGCCTCTGGCTGCTGCTGCTGCCC
original cDNA sequence snippet CCATGGGGCCCCGGCTCAGCGTCTGGCTGCTGCTGCTGCCC
altered cDNA sequence snippet CCATGGGGCCCCGGCTCAGCCTCTGGCTGCTGCTGCTGCCC
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 MGPRLSLWLL 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*
speed 0.25 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.997085450673265 (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) chr13:110959356C>GN/A show variant in all transcripts   IGV
HGNC symbol COL4A1
Ensembl transcript ID ENST00000397198
Genbank transcript ID N/A
UniProt peptide P02462
alteration type single base exchange
alteration region CDS
DNA changes c.19G>C
cDNA.141G>C
g.141G>C
AA changes V7L Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 7
frameshift no
known variant Reference ID: rs9515185
databasehomozygous (G/G)heterozygousallele carriers
1000G52010841604
ExAC125625193775
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7720.991
0.3150.972
(flanking)0.330.957
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased144wt: 0.57 / mu: 0.68wt: TGGGGCCCCGGCTCAGCGTCTGGCTGCTGCTGCTGCCCGCC
mu: TGGGGCCCCGGCTCAGCCTCTGGCTGCTGCTGCTGCCCGCC		 gtct|GGCT
Acc gained1520.37mu: CGGCTCAGCCTCTGGCTGCTGCTGCTGCCCGCCGCCCTTCT gctg|CTGC
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      7 MGPRLSVWLLLLPAALLLH
mutated  all conserved    7 MGPRLSLWLLLLPAALLLHEEH
Ptroglodytes  all identical  ENSPTRG00000006031  7 MGPRLSVWLLLLPAALLLHEEH
Mmulatta  no alignment  ENSMMUG00000022280  n/a
Fcatus  no alignment  ENSFCAG00000014784  n/a
Mmusculus  all identical  ENSMUSG00000031502  7 MGPRLSVWLLLLFAALLLHEER
Ggallus  no alignment  ENSGALG00000016841  n/a
Trubripes  no alignment  ENSTRUG00000006458  n/a
Drerio  no alignment  ENSDARG00000055009  n/a
Dmelanogaster  no homologue    
Celegans  all conserved  F01G12.5  13 LGPVLRLAILALLAVSYVQSQ-
Xtropicalis  no alignment  ENSXETG00000002637  n/a
protein features
start (aa)end (aa)featuredetails 
127SIGNALlost
28172PROPEPN-terminal propeptide (7S domain). /FTId=PRO_0000005748.might get lost (downstream of altered splice site)
126126CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
1731440REGIONTriple-helical region.might get lost (downstream of altered splice site)
237238CONFLICTSG -> KE (in Ref. 6; AA sequence).might get lost (downstream of altered splice site)
241241CONFLICTG -> K (in Ref. 6; AA sequence).might get lost (downstream of altered splice site)
319319CONFLICTQ -> A (in Ref. 4; CAA29075).might get lost (downstream of altered splice site)
719719CONFLICTN -> D (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
837837CONFLICTD -> Y (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
842842CONFLICTK -> P (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
896896CONFLICTV -> W (in Ref. 7; CAA68698).might get lost (downstream of altered splice site)
904904CONFLICTE -> Q (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
914914CONFLICTS -> K (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
998998CONFLICTS -> K (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
10101010CONFLICTK -> P (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
10121012CONFLICTS -> K (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
13581358CONFLICTE -> Q (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
14451669DOMAINCollagen IV NC1.might get lost (downstream of altered splice site)
14461451STRANDmight get lost (downstream of altered splice site)
14531456STRANDmight get lost (downstream of altered splice site)
14601460DISULFIDmight get lost (downstream of altered splice site)
14651478STRANDmight get lost (downstream of altered splice site)
14811484STRANDmight get lost (downstream of altered splice site)
14901490CONFLICTA -> T (in Ref. 17; ABE73157).might get lost (downstream of altered splice site)
14901492HELIXmight get lost (downstream of altered splice site)
14931493DISULFIDmight get lost (downstream of altered splice site)
14931496STRANDmight get lost (downstream of altered splice site)
15021505STRANDmight get lost (downstream of altered splice site)
15051505DISULFIDmight get lost (downstream of altered splice site)
15071507CONFLICTI -> T (in Ref. 17; ABE73157).might get lost (downstream of altered splice site)
15091514STRANDmight get lost (downstream of altered splice site)
15111511DISULFIDmight get lost (downstream of altered splice site)
15191519CONFLICTY -> C (in Ref. 17; ABE73157).might get lost (downstream of altered splice site)
15191524STRANDmight get lost (downstream of altered splice site)
15331533CROSSLNKS-Lysyl-methionine sulfilimine (Met-Lys) (interchain with K-1651).might get lost (downstream of altered splice site)
15381544HELIXmight get lost (downstream of altered splice site)
15471555STRANDmight get lost (downstream of altered splice site)
15481548DISULFIDmight get lost (downstream of altered splice site)
15511551DISULFIDmight get lost (downstream of altered splice site)
15571561STRANDmight get lost (downstream of altered splice site)
15631566STRANDmight get lost (downstream of altered splice site)
15701570CONFLICTC -> Y (in Ref. 16; AAM97359).might get lost (downstream of altered splice site)
15701570DISULFIDmight get lost (downstream of altered splice site)
15741587STRANDmight get lost (downstream of altered splice site)
15891591HELIXmight get lost (downstream of altered splice site)
15931595STRANDmight get lost (downstream of altered splice site)
16011603HELIXmight get lost (downstream of altered splice site)
16041604DISULFIDmight get lost (downstream of altered splice site)
16041607STRANDmight get lost (downstream of altered splice site)
16131617STRANDmight get lost (downstream of altered splice site)
16161616DISULFIDmight get lost (downstream of altered splice site)
16201623STRANDmight get lost (downstream of altered splice site)
16221622DISULFIDmight get lost (downstream of altered splice site)
16291634STRANDmight get lost (downstream of altered splice site)
16381640HELIXmight get lost (downstream of altered splice site)
16481651STRANDmight get lost (downstream of altered splice site)
16511651CROSSLNKS-Lysyl-methionine sulfilimine (Lys-Met) (interchain with M-1533).might get lost (downstream of altered splice site)
16551658HELIXmight get lost (downstream of altered splice site)
16611667STRANDmight get lost (downstream of altered splice site)
16621662DISULFIDmight get lost (downstream of altered splice site)
16651665DISULFIDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3957 / 3957
position (AA) of stopcodon in wt / mu AA sequence 1319 / 1319
position of stopcodon in wt / mu cDNA 4079 / 4079
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 13
strand -1
last intron/exon boundary 3998
theoretical NMD boundary in CDS 3825
length of CDS 3957
coding sequence (CDS) position 19
cDNA position
(for ins/del: last normal base / first normal base)		 141
gDNA position
(for ins/del: last normal base / first normal base)		 141
chromosomal position
(for ins/del: last normal base / first normal base)		 110959356
original gDNA sequence snippet CCATGGGGCCCCGGCTCAGCGTCTGGCTGCTGCTGCTGCCC
altered gDNA sequence snippet CCATGGGGCCCCGGCTCAGCCTCTGGCTGCTGCTGCTGCCC
original cDNA sequence snippet CCATGGGGCCCCGGCTCAGCGTCTGGCTGCTGCTGCTGCCC
altered cDNA sequence snippet CCATGGGGCCCCGGCTCAGCCTCTGGCTGCTGCTGCTGCCC
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 MGPRLSLWLL 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*
speed 0.27 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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.997085450673265 (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) chr13:110959356C>GN/A show variant in all transcripts   IGV
HGNC symbol COL4A1
Ensembl transcript ID ENST00000543140
Genbank transcript ID N/A
UniProt peptide P02462
alteration type single base exchange
alteration region CDS
DNA changes c.19G>C
cDNA.123G>C
g.141G>C
AA changes V7L Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 7
frameshift no
known variant Reference ID: rs9515185
databasehomozygous (G/G)heterozygousallele carriers
1000G52010841604
ExAC125625193775
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7720.991
0.3150.972
(flanking)0.330.957
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased144wt: 0.57 / mu: 0.68wt: TGGGGCCCCGGCTCAGCGTCTGGCTGCTGCTGCTGCCCGCC
mu: TGGGGCCCCGGCTCAGCCTCTGGCTGCTGCTGCTGCCCGCC		 gtct|GGCT
Acc gained1520.37mu: CGGCTCAGCCTCTGGCTGCTGCTGCTGCCCGCCGCCCTTCT gctg|CTGC
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      7 MGPRLSVWLLLLPAALLLH
mutated  all conserved    7 MGPRLSLWLLLLPAALLLHEEH
Ptroglodytes  all identical  ENSPTRG00000006031  7 MGPRLSVWLLLLPAALLLHEEH
Mmulatta  no alignment  ENSMMUG00000022280  n/a
Fcatus  no alignment  ENSFCAG00000014784  n/a
Mmusculus  all identical  ENSMUSG00000031502  7 MGPRLSVWLLLLFAALLLHEER
Ggallus  no alignment  ENSGALG00000016841  n/a
Trubripes  no alignment  ENSTRUG00000006458  n/a
Drerio  no alignment  ENSDARG00000055009  n/a
Dmelanogaster  no homologue    
Celegans  all conserved  F01G12.5  13 LGPVLRLAILALLAVSYVQSQ-
Xtropicalis  no alignment  ENSXETG00000002637  n/a
protein features
start (aa)end (aa)featuredetails 
127SIGNALlost
28172PROPEPN-terminal propeptide (7S domain). /FTId=PRO_0000005748.might get lost (downstream of altered splice site)
126126CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
1731440REGIONTriple-helical region.might get lost (downstream of altered splice site)
237238CONFLICTSG -> KE (in Ref. 6; AA sequence).might get lost (downstream of altered splice site)
241241CONFLICTG -> K (in Ref. 6; AA sequence).might get lost (downstream of altered splice site)
319319CONFLICTQ -> A (in Ref. 4; CAA29075).might get lost (downstream of altered splice site)
719719CONFLICTN -> D (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
837837CONFLICTD -> Y (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
842842CONFLICTK -> P (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
896896CONFLICTV -> W (in Ref. 7; CAA68698).might get lost (downstream of altered splice site)
904904CONFLICTE -> Q (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
914914CONFLICTS -> K (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
998998CONFLICTS -> K (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
10101010CONFLICTK -> P (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
10121012CONFLICTS -> K (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
13581358CONFLICTE -> Q (in Ref. 8; AA sequence).might get lost (downstream of altered splice site)
14451669DOMAINCollagen IV NC1.might get lost (downstream of altered splice site)
14461451STRANDmight get lost (downstream of altered splice site)
14531456STRANDmight get lost (downstream of altered splice site)
14601460DISULFIDmight get lost (downstream of altered splice site)
14651478STRANDmight get lost (downstream of altered splice site)
14811484STRANDmight get lost (downstream of altered splice site)
14901490CONFLICTA -> T (in Ref. 17; ABE73157).might get lost (downstream of altered splice site)
14901492HELIXmight get lost (downstream of altered splice site)
14931493DISULFIDmight get lost (downstream of altered splice site)
14931496STRANDmight get lost (downstream of altered splice site)
15021505STRANDmight get lost (downstream of altered splice site)
15051505DISULFIDmight get lost (downstream of altered splice site)
15071507CONFLICTI -> T (in Ref. 17; ABE73157).might get lost (downstream of altered splice site)
15091514STRANDmight get lost (downstream of altered splice site)
15111511DISULFIDmight get lost (downstream of altered splice site)
15191519CONFLICTY -> C (in Ref. 17; ABE73157).might get lost (downstream of altered splice site)
15191524STRANDmight get lost (downstream of altered splice site)
15331533CROSSLNKS-Lysyl-methionine sulfilimine (Met-Lys) (interchain with K-1651).might get lost (downstream of altered splice site)
15381544HELIXmight get lost (downstream of altered splice site)
15471555STRANDmight get lost (downstream of altered splice site)
15481548DISULFIDmight get lost (downstream of altered splice site)
15511551DISULFIDmight get lost (downstream of altered splice site)
15571561STRANDmight get lost (downstream of altered splice site)
15631566STRANDmight get lost (downstream of altered splice site)
15701570CONFLICTC -> Y (in Ref. 16; AAM97359).might get lost (downstream of altered splice site)
15701570DISULFIDmight get lost (downstream of altered splice site)
15741587STRANDmight get lost (downstream of altered splice site)
15891591HELIXmight get lost (downstream of altered splice site)
15931595STRANDmight get lost (downstream of altered splice site)
16011603HELIXmight get lost (downstream of altered splice site)
16041604DISULFIDmight get lost (downstream of altered splice site)
16041607STRANDmight get lost (downstream of altered splice site)
16131617STRANDmight get lost (downstream of altered splice site)
16161616DISULFIDmight get lost (downstream of altered splice site)
16201623STRANDmight get lost (downstream of altered splice site)
16221622DISULFIDmight get lost (downstream of altered splice site)
16291634STRANDmight get lost (downstream of altered splice site)
16381640HELIXmight get lost (downstream of altered splice site)
16481651STRANDmight get lost (downstream of altered splice site)
16511651CROSSLNKS-Lysyl-methionine sulfilimine (Lys-Met) (interchain with M-1533).might get lost (downstream of altered splice site)
16551658HELIXmight get lost (downstream of altered splice site)
16611667STRANDmight get lost (downstream of altered splice site)
16621662DISULFIDmight get lost (downstream of altered splice site)
16651665DISULFIDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1560 / 1560
position (AA) of stopcodon in wt / mu AA sequence 520 / 520
position of stopcodon in wt / mu cDNA 1664 / 1664
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 105 / 105
chromosome 13
strand -1
last intron/exon boundary 1641
theoretical NMD boundary in CDS 1486
length of CDS 1560
coding sequence (CDS) position 19
cDNA position
(for ins/del: last normal base / first normal base)		 123
gDNA position
(for ins/del: last normal base / first normal base)		 141
chromosomal position
(for ins/del: last normal base / first normal base)		 110959356
original gDNA sequence snippet CCATGGGGCCCCGGCTCAGCGTCTGGCTGCTGCTGCTGCCC
altered gDNA sequence snippet CCATGGGGCCCCGGCTCAGCCTCTGGCTGCTGCTGCTGCCC
original cDNA sequence snippet CCATGGGGCCCCGGCTCAGCGTCTGGCTGCTGCTGCTGCCC
altered cDNA sequence snippet CCATGGGGCCCCGGCTCAGCCTCTGGCTGCTGCTGCTGCCC
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 VPLLFQIHK*
mutated AA sequence MGPRLSLWLL 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 VPLLFQIHK*
speed 0.12 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

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