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MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000225964
MT speed 0 s - this script 2.932713 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
COL1A1disease_causing_automatic0.999999997989764simple_aaeaffected0G926Csingle base exchangers72653154show file

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997989764 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM870006)
  • known disease mutation: rs17294 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:48266791C>AN/A show variant in all transcripts   IGV
HGNC symbol COL1A1
Ensembl transcript ID ENST00000225964
Genbank transcript ID NM_000088
UniProt peptide P02452
alteration type single base exchange
alteration region CDS
DNA changes c.2776G>T
cDNA.2895G>T
g.12203G>T
AA changes G926C Score: 159 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 926
frameshift no
known variant Reference ID: rs72653154
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17294 (pathogenic for Osteogenesis imperfecta, recessive perinatal lethal) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM870006)

known disease mutation at this position, please check HGMD for details (HGMD ID CM870006)
known disease mutation at this position, please check HGMD for details (HGMD ID CM870006)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.4291
5.4291
(flanking)-0.2180.967
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased12203wt: 0.30 / mu: 0.35wt: CTGGTGAAGTTGGTCCCCCTGGTCCCCCTGGCCCTGCTGGC
mu: CTGGTGAAGTTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGC		 cctg|GTCC
Acc marginally increased12213wt: 0.9077 / mu: 0.9559 (marginal change - not scored)wt: TGGTCCCCCTGGTCCCCCTGGCCCTGCTGGCGAGAAAGGAT
mu: TGGTCCCCCTTGTCCCCCTGGCCCTGCTGGCGAGAAAGGAT		 ctgg|CCCT
Acc marginally increased12212wt: 0.8836 / mu: 0.9665 (marginal change - not scored)wt: TTGGTCCCCCTGGTCCCCCTGGCCCTGCTGGCGAGAAAGGA
mu: TTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGCGAGAAAGGA		 cctg|GCCC
Acc increased12207wt: 0.34 / mu: 0.83wt: TGAAGTTGGTCCCCCTGGTCCCCCTGGCCCTGCTGGCGAGA
mu: TGAAGTTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGCGAGA		 gtcc|CCCT
Acc increased12210wt: 0.31 / mu: 0.64wt: AGTTGGTCCCCCTGGTCCCCCTGGCCCTGCTGGCGAGAAAG
mu: AGTTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGCGAGAAAG		 cccc|TGGC
Acc increased12211wt: 0.86 / mu: 0.97wt: GTTGGTCCCCCTGGTCCCCCTGGCCCTGCTGGCGAGAAAGG
mu: GTTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGCGAGAAAGG		 ccct|GGCC
Acc gained122090.33mu: AAGTTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGCGAGAAA cccc|CTGG
Acc gained122050.30mu: GGTGAAGTTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGCGA ttgt|CCCC
Acc gained122080.68mu: GAAGTTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGCGAGAA tccc|CCTG
distance from splice site 54
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      926PAGRPGEVGPPGPPGPAGEKGSPG
mutated  not conserved    926PAGRPGEVGPPCPPGPAGEKGSP
Ptroglodytes  all identical  ENSPTRG00000009393  926PAGRPGEVGPPGPPGPAGEKGSP
Mmulatta  all identical  ENSMMUG00000001467  926PAGRPGEVGPPGPPGPAGEKGSP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000001506  915PAGRPGEVGPPGPPGPAGEKGSP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007520  919PAGRPGEAGAVGAPGPSGEKGSP
Drerio  all identical  ENSDARG00000012405  910PAGRTGEVGAAGPPGAPGEKGNP
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003374  912PAGRPGEPGAAGPSGPPGEKGSP
protein features
start (aa)end (aa)featuredetails 
1791192REGIONTriple-helical region.lost
953954SITECleavage; by collagenase (By similarity).might get lost (downstream of altered splice site)
966968STRANDmight get lost (downstream of altered splice site)
975976CONFLICTLP -> PL (in Ref. 19; AAA52291).might get lost (downstream of altered splice site)
10811081CONFLICTV -> A (in Ref. 18; AAA51995).might get lost (downstream of altered splice site)
10931095MOTIFCell attachment site (Potential).might get lost (downstream of altered splice site)
11081108CARBOHYDO-linked (Gal...) (By similarity).might get lost (downstream of altered splice site)
11081108MOD_RES5-hydroxylysine (By similarity).might get lost (downstream of altered splice site)
11641164MOD_RES3-hydroxyproline (By similarity).might get lost (downstream of altered splice site)
11931218REGIONNonhelical region (C-terminal).might get lost (downstream of altered splice site)
12081208MOD_RESAllysine (By similarity).might get lost (downstream of altered splice site)
12181219SITECleavage; by procollagen C-endopeptidase.might get lost (downstream of altered splice site)
12191464PROPEPC-terminal propeptide. /FTId=PRO_0000005721.might get lost (downstream of altered splice site)
12291464DOMAINFibrillar collagen NC1.might get lost (downstream of altered splice site)
12591259DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
12591259DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
12651265DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
12651265DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
12821282DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
12821282DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
12911291DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
12911291DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
12991299DISULFIDBy similarity.might get lost (downstream of altered splice site)
13291329CONFLICTS -> T (in Ref. 25; AAB27856).might get lost (downstream of altered splice site)
13651365CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
13701370DISULFIDBy similarity.might get lost (downstream of altered splice site)
14151415DISULFIDBy similarity.might get lost (downstream of altered splice site)
14621462DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4395 / 4395
position (AA) of stopcodon in wt / mu AA sequence 1465 / 1465
position of stopcodon in wt / mu cDNA 4514 / 4514
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 120 / 120
chromosome 17
strand -1
last intron/exon boundary 4368
theoretical NMD boundary in CDS 4198
length of CDS 4395
coding sequence (CDS) position 2776
cDNA position
(for ins/del: last normal base / first normal base)		 2895
gDNA position
(for ins/del: last normal base / first normal base)		 12203
chromosomal position
(for ins/del: last normal base / first normal base)		 48266791
original gDNA sequence snippet CTGGTGAAGTTGGTCCCCCTGGTCCCCCTGGCCCTGCTGGC
altered gDNA sequence snippet CTGGTGAAGTTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGC
original cDNA sequence snippet CTGGTGAAGTTGGTCCCCCTGGTCCCCCTGGCCCTGCTGGC
altered cDNA sequence snippet CTGGTGAAGTTGGTCCCCCTTGTCCCCCTGGCCCTGCTGGC
wildtype AA sequence MFSFVDLRLL LLLAATALLT HGQEEGQVEG QDEDIPPITC VQNGLRYHDR DVWKPEPCRI
CVCDNGKVLC DDVICDETKN CPGAEVPEGE CCPVCPDGSE SPTDQETTGV EGPKGDTGPR
GPRGPAGPPG RDGIPGQPGL PGPPGPPGPP GPPGLGGNFA PQLSYGYDEK STGGISVPGP
MGPSGPRGLP GPPGAPGPQG FQGPPGEPGE PGASGPMGPR GPPGPPGKNG DDGEAGKPGR
PGERGPPGPQ GARGLPGTAG LPGMKGHRGF SGLDGAKGDA GPAGPKGEPG SPGENGAPGQ
MGPRGLPGER GRPGAPGPAG ARGNDGATGA AGPPGPTGPA GPPGFPGAVG AKGEAGPQGP
RGSEGPQGVR GEPGPPGPAG AAGPAGNPGA DGQPGAKGAN GAPGIAGAPG FPGARGPSGP
QGPGGPPGPK GNSGEPGAPG SKGDTGAKGE PGPVGVQGPP GPAGEEGKRG ARGEPGPTGL
PGPPGERGGP GSRGFPGADG VAGPKGPAGE RGSPGPAGPK GSPGEAGRPG EAGLPGAKGL
TGSPGSPGPD GKTGPPGPAG QDGRPGPPGP PGARGQAGVM GFPGPKGAAG EPGKAGERGV
PGPPGAVGPA GKDGEAGAQG PPGPAGPAGE RGEQGPAGSP GFQGLPGPAG PPGEAGKPGE
QGVPGDLGAP GPSGARGERG FPGERGVQGP PGPAGPRGAN GAPGNDGAKG DAGAPGAPGS
QGAPGLQGMP GERGAAGLPG PKGDRGDAGP KGADGSPGKD GVRGLTGPIG PPGPAGAPGD
KGESGPSGPA GPTGARGAPG DRGEPGPPGP AGFAGPPGAD GQPGAKGEPG DAGAKGDAGP
PGPAGPAGPP GPIGNVGAPG AKGARGSAGP PGATGFPGAA GRVGPPGPSG NAGPPGPPGP
AGKEGGKGPR GETGPAGRPG EVGPPGPPGP AGEKGSPGAD GPAGAPGTPG PQGIAGQRGV
VGLPGQRGER GFPGLPGPSG EPGKQGPSGA SGERGPPGPM GPPGLAGPPG ESGREGAPGA
EGSPGRDGSP GAKGDRGETG PAGPPGAPGA PGAPGPVGPA GKSGDRGETG PAGPTGPVGP
VGARGPAGPQ GPRGDKGETG EQGDRGIKGH RGFSGLQGPP GPPGSPGEQG PSGASGPAGP
RGPPGSAGAP GKDGLNGLPG PIGPPGPRGR TGDAGPVGPP GPPGPPGPPG PPSAGFDFSF
LPQPPQEKAH DGGRYYRADD ANVVRDRDLE VDTTLKSLSQ QIENIRSPEG SRKNPARTCR
DLKMCHSDWK SGEYWIDPNQ GCNLDAIKVF CNMETGETCV YPTQPSVAQK NWYISKNPKD
KRHVWFGESM TDGFQFEYGG QGSDPADVAI QLTFLRLMST EASQNITYHC KNSVAYMDQQ
TGNLKKALLL QGSNEIEIRA EGNSRFTYSV TVDGCTSHTG AWGKTVIEYK TTKTSRLPII
DVAPLDVGAP DQEFGFDVGP VCFL*
mutated AA sequence MFSFVDLRLL LLLAATALLT HGQEEGQVEG QDEDIPPITC VQNGLRYHDR DVWKPEPCRI
CVCDNGKVLC DDVICDETKN CPGAEVPEGE CCPVCPDGSE SPTDQETTGV EGPKGDTGPR
GPRGPAGPPG RDGIPGQPGL PGPPGPPGPP GPPGLGGNFA PQLSYGYDEK STGGISVPGP
MGPSGPRGLP GPPGAPGPQG FQGPPGEPGE PGASGPMGPR GPPGPPGKNG DDGEAGKPGR
PGERGPPGPQ GARGLPGTAG LPGMKGHRGF SGLDGAKGDA GPAGPKGEPG SPGENGAPGQ
MGPRGLPGER GRPGAPGPAG ARGNDGATGA AGPPGPTGPA GPPGFPGAVG AKGEAGPQGP
RGSEGPQGVR GEPGPPGPAG AAGPAGNPGA DGQPGAKGAN GAPGIAGAPG FPGARGPSGP
QGPGGPPGPK GNSGEPGAPG SKGDTGAKGE PGPVGVQGPP GPAGEEGKRG ARGEPGPTGL
PGPPGERGGP GSRGFPGADG VAGPKGPAGE RGSPGPAGPK GSPGEAGRPG EAGLPGAKGL
TGSPGSPGPD GKTGPPGPAG QDGRPGPPGP PGARGQAGVM GFPGPKGAAG EPGKAGERGV
PGPPGAVGPA GKDGEAGAQG PPGPAGPAGE RGEQGPAGSP GFQGLPGPAG PPGEAGKPGE
QGVPGDLGAP GPSGARGERG FPGERGVQGP PGPAGPRGAN GAPGNDGAKG DAGAPGAPGS
QGAPGLQGMP GERGAAGLPG PKGDRGDAGP KGADGSPGKD GVRGLTGPIG PPGPAGAPGD
KGESGPSGPA GPTGARGAPG DRGEPGPPGP AGFAGPPGAD GQPGAKGEPG DAGAKGDAGP
PGPAGPAGPP GPIGNVGAPG AKGARGSAGP PGATGFPGAA GRVGPPGPSG NAGPPGPPGP
AGKEGGKGPR GETGPAGRPG EVGPPCPPGP AGEKGSPGAD GPAGAPGTPG PQGIAGQRGV
VGLPGQRGER GFPGLPGPSG EPGKQGPSGA SGERGPPGPM GPPGLAGPPG ESGREGAPGA
EGSPGRDGSP GAKGDRGETG PAGPPGAPGA PGAPGPVGPA GKSGDRGETG PAGPTGPVGP
VGARGPAGPQ GPRGDKGETG EQGDRGIKGH RGFSGLQGPP GPPGSPGEQG PSGASGPAGP
RGPPGSAGAP GKDGLNGLPG PIGPPGPRGR TGDAGPVGPP GPPGPPGPPG PPSAGFDFSF
LPQPPQEKAH DGGRYYRADD ANVVRDRDLE VDTTLKSLSQ QIENIRSPEG SRKNPARTCR
DLKMCHSDWK SGEYWIDPNQ GCNLDAIKVF CNMETGETCV YPTQPSVAQK NWYISKNPKD
KRHVWFGESM TDGFQFEYGG QGSDPADVAI QLTFLRLMST EASQNITYHC KNSVAYMDQQ
TGNLKKALLL QGSNEIEIRA EGNSRFTYSV TVDGCTSHTG AWGKTVIEYK TTKTSRLPII
DVAPLDVGAP DQEFGFDVGP VCFL*
speed 0.82 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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