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MutationTaster - study a chromosomal position

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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: ENST00000264828
MT speed 1.27 s - this script 4.597514 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
COL5A3polymorphism_automatic7.10139455419867e-05simple_aaeaffectedA1488Psingle base exchangers3745584show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.999928986054458 (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) chr19:10077419C>GN/A show variant in all transcripts   IGV
HGNC symbol COL5A3
Ensembl transcript ID ENST00000264828
Genbank transcript ID NM_015719
UniProt peptide P25940
alteration type single base exchange
alteration region CDS
DNA changes c.4462G>C
cDNA.4548G>C
g.43729G>C
AA changes A1488P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS
1488
frameshift no
known variant Reference ID: rs3745584
databasehomozygous (G/G)heterozygousallele carriers
1000G38510641449
ExAC137928774256
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)3.4990.754
0.1010.757
(flanking)0.1780.813
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased43723wt: 0.6721 / mu: 0.7241 (marginal change - not scored)wt: CCGTCCCCATCCCCTACGCCCAGGGTGCCCCTGCCGAGCTG
mu: CCGTCCCCATCCCCTACGCCCAGGGTCCCCCTGCCGAGCTG
 gccc|AGGG
Acc marginally increased43724wt: 0.8600 / mu: 0.8980 (marginal change - not scored)wt: CGTCCCCATCCCCTACGCCCAGGGTGCCCCTGCCGAGCTGC
mu: CGTCCCCATCCCCTACGCCCAGGGTCCCCCTGCCGAGCTGC
 ccca|GGGT
Acc increased43739wt: 0.61 / mu: 0.77wt: CGCCCAGGGTGCCCCTGCCGAGCTGCATGGGCTGCGCAGGC
mu: CGCCCAGGGTCCCCCTGCCGAGCTGCATGGGCTGCGCAGGC
 ccga|GCTG
Acc marginally increased43725wt: 0.3883 / mu: 0.4322 (marginal change - not scored)wt: GTCCCCATCCCCTACGCCCAGGGTGCCCCTGCCGAGCTGCA
mu: GTCCCCATCCCCTACGCCCAGGGTCCCCCTGCCGAGCTGCA
 ccag|GGTG
Donor increased43721wt: 0.30 / mu: 0.43wt: CTACGCCCAGGGTGC
mu: CTACGCCCAGGGTCC
 ACGC|ccag
Donor marginally increased43734wt: 0.9346 / mu: 0.9512 (marginal change - not scored)wt: GCCCCTGCCGAGCTG
mu: CCCCCTGCCGAGCTG
 CCCT|gccg
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1488TGPAGPPGPPGAPAELHGLRRRRR
mutated  not conserved    1488TGPAGPPGPPGPPAELHGLRRRR
Ptroglodytes  not conserved  ENSPTRG00000010454  1370TGPAGPPGPPGPPAE
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000004098  1487PGPAGPPGPPGSPAEVHGLRRR
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000005692  1559PPATAIEPLPMREGRRNRR
Drerio  not conserved  ENSDARG00000017360  1247TGPAGPPGPPGPPAAMIEPLPIREGRKKRR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000011757  1107PGSAGPPGPPGPPAQFIQPLPYEGTRKRR
protein features
start (aa)end (aa)featuredetails 
3921489REGIONTriple-helical region.lost
14301488DOMAINCollagen-like 6.lost
15141744DOMAINFibrillar collagen NC1.might get lost (downstream of altered splice site)
15441544DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15441544DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15671567DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15671567DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15761576DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15761576DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15851585DISULFIDBy similarity.might get lost (downstream of altered splice site)
16511651DISULFIDBy similarity.might get lost (downstream of altered splice site)
16871687CONFLICTA -> T (in Ref. 1; AAF59902).might get lost (downstream of altered splice site)
16961696DISULFIDBy similarity.might get lost (downstream of altered splice site)
17421742DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5238 / 5238
position (AA) of stopcodon in wt / mu AA sequence 1746 / 1746
position of stopcodon in wt / mu cDNA 5324 / 5324
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 87 / 87
chromosome 19
strand -1
last intron/exon boundary 5178
theoretical NMD boundary in CDS 5041
length of CDS 5238
coding sequence (CDS) position 4462
cDNA position
(for ins/del: last normal base / first normal base)
4548
gDNA position
(for ins/del: last normal base / first normal base)
43729
chromosomal position
(for ins/del: last normal base / first normal base)
10077419
original gDNA sequence snippet CCATCCCCTACGCCCAGGGTGCCCCTGCCGAGCTGCATGGG
altered gDNA sequence snippet CCATCCCCTACGCCCAGGGTCCCCCTGCCGAGCTGCATGGG
original cDNA sequence snippet GCCCACCAGGCCCCCCGGGTGCCCCTGCCGAGCTGCATGGG
altered cDNA sequence snippet GCCCACCAGGCCCCCCGGGTCCCCCTGCCGAGCTGCATGGG
wildtype AA sequence MGNRRDLGQP RAGLCLLLAA LQLLPGTQAD PVDVLKALGV QGGQAGVPEG PGFCPQRTPE
GDRAFRIGQA STLGIPTWEL FPEGHFPENF SLLITLRGQP ANQSVLLSIY DERGARQLGL
ALGPALGLLG DPFRPLPQQV NLTDGRWHRV AVSIDGEMVT LVADCEAQPP VLGHGPRFIS
IAGLTVLGTQ DLGEKTFEGD IQELLISPDP QAAFQACERY LPDCDNLAPA ATVAPQGEPE
TPRPRRKGKG KGRKKGRGRK GKGRKKNKEI WTSSPPPDSA ENQTSTDIPK TETPAPNLPP
TPTPLVVTST VTTGLNATIL ERSLDPDSGT ELGTLETKAA REDEEGDDST MGPDFRAAEY
PSRTQFQIFP GAGEKGAKGE PAVIEKGQQF EGPPGAPGPQ GVVGPSGPPG PPGFPGDPGP
PGPAGLPGIP GIDGIRGPPG TVIMMPFQFA GGSFKGPPVS FQQAQAQAVL QQTQLSMKGP
PGPVGLTGRP GPVGLPGHPG LKGEEGAEGP QGPRGLQGPH GPPGRVGKMG RPGADGARGL
PGDTGPKGDR GFDGLPGLPG EKGQRGDFGH VGQPGPPGED GERGAEGPPG PTGQAGEPGP
RGLLGPRGSP GPTGRPGVTG IDGAPGAKGN VGPPGEPGPP GQQGNHGSQG LPGPQGLIGT
PGEKGPPGNP GIPGLPGSDG PLGHPGHEGP TGEKGAQGPP GSAGPPGYPG PRGVKGTSGN
RGLQGEKGEK GEDGFPGFKG DVGLKGDQGK PGAPGPRGED GPEGPKGQAG QAGEEGPPGS
AGEKGKLGVP GLPGYPGRPG PKGSIGFPGP LGPIGEKGKS GKTGQPGLEG ERGPPGSRGE
RGQPGATGQP GPKGDVGQDG APGIPGEKGL PGLQGPPGFP GPKGPPGHQG KDGRPGHPGQ
RGELGFQGQT GPPGPAGVLG PQGKTGEVGP LGERGPPGPP GPPGEQGLPG LEGREGAKGE
LGPPGPLGKE GPAGLRGFPG PKGGPGDPGP TGLKGDKGPP GPVGANGSPG ERGPLGPAGG
IGLPGQSGSE GPVGPAGKKG SRGERGPPGP TGKDGIPGPL GPLGPPGAAG PSGEEGDKGD
VGAPGHKGSK GDKGDAGPPG QPGIRGPAGH PGPPGADGAQ GRRGPPGLFG QKGDDGVRGF
VGVIGPPGLQ GLPGPPGEKG EVGDVGSMGP HGAPGPRGPQ GPTGSEGTPG LPGGVGQPGA
VGEKGERGDA GDPGPPGAPG IPGPKGDIGE KGDSGPSGAA GPPGKKGPPG EDGAKGSVGP
TGLPGDLGPP GDPGVSGIDG SPGEKGDPGD VGGPGPPGAS GEPGAPGPPG KRGPSGHMGR
EGREGEKGAK GEPGPDGPPG RTGPMGARGP PGRVGPEGLR GIPGPVGEPG LLGAPGQMGP
PGPLGPSGLP GLKGDTGPKG EKGHIGLIGL IGPPGEAGEK GDQGLPGVQG PPGPKGDPGP
PGPIGSLGHP GPPGVAGPLG QKGSKGSPGS MGPRGDTGPA GPPGPPGAPA ELHGLRRRRR
FVPVPLPVVE GGLEEVLASL TSLSLELEQL RRPPGTAERP GLVCHELHRN HPHLPDGEYW
IDPNQGCARD SFRVFCNFTA GGETCLYPDK KFEIVKLASW SKEKPGGWYS TFRRGKKFSY
VDADGSPVNV VQLNFLKLLS ATARQNFTYS CQNAAAWLDE ATGDYSHSAR FLGTNGEELS
FNQTTAATVS VPQDGCRLRK GQTKTLFEFS SSRAGFLPLW DVAATDFGQT NQKFGFELGP
VCFSS*
mutated AA sequence MGNRRDLGQP RAGLCLLLAA LQLLPGTQAD PVDVLKALGV QGGQAGVPEG PGFCPQRTPE
GDRAFRIGQA STLGIPTWEL FPEGHFPENF SLLITLRGQP ANQSVLLSIY DERGARQLGL
ALGPALGLLG DPFRPLPQQV NLTDGRWHRV AVSIDGEMVT LVADCEAQPP VLGHGPRFIS
IAGLTVLGTQ DLGEKTFEGD IQELLISPDP QAAFQACERY LPDCDNLAPA ATVAPQGEPE
TPRPRRKGKG KGRKKGRGRK GKGRKKNKEI WTSSPPPDSA ENQTSTDIPK TETPAPNLPP
TPTPLVVTST VTTGLNATIL ERSLDPDSGT ELGTLETKAA REDEEGDDST MGPDFRAAEY
PSRTQFQIFP GAGEKGAKGE PAVIEKGQQF EGPPGAPGPQ GVVGPSGPPG PPGFPGDPGP
PGPAGLPGIP GIDGIRGPPG TVIMMPFQFA GGSFKGPPVS FQQAQAQAVL QQTQLSMKGP
PGPVGLTGRP GPVGLPGHPG LKGEEGAEGP QGPRGLQGPH GPPGRVGKMG RPGADGARGL
PGDTGPKGDR GFDGLPGLPG EKGQRGDFGH VGQPGPPGED GERGAEGPPG PTGQAGEPGP
RGLLGPRGSP GPTGRPGVTG IDGAPGAKGN VGPPGEPGPP GQQGNHGSQG LPGPQGLIGT
PGEKGPPGNP GIPGLPGSDG PLGHPGHEGP TGEKGAQGPP GSAGPPGYPG PRGVKGTSGN
RGLQGEKGEK GEDGFPGFKG DVGLKGDQGK PGAPGPRGED GPEGPKGQAG QAGEEGPPGS
AGEKGKLGVP GLPGYPGRPG PKGSIGFPGP LGPIGEKGKS GKTGQPGLEG ERGPPGSRGE
RGQPGATGQP GPKGDVGQDG APGIPGEKGL PGLQGPPGFP GPKGPPGHQG KDGRPGHPGQ
RGELGFQGQT GPPGPAGVLG PQGKTGEVGP LGERGPPGPP GPPGEQGLPG LEGREGAKGE
LGPPGPLGKE GPAGLRGFPG PKGGPGDPGP TGLKGDKGPP GPVGANGSPG ERGPLGPAGG
IGLPGQSGSE GPVGPAGKKG SRGERGPPGP TGKDGIPGPL GPLGPPGAAG PSGEEGDKGD
VGAPGHKGSK GDKGDAGPPG QPGIRGPAGH PGPPGADGAQ GRRGPPGLFG QKGDDGVRGF
VGVIGPPGLQ GLPGPPGEKG EVGDVGSMGP HGAPGPRGPQ GPTGSEGTPG LPGGVGQPGA
VGEKGERGDA GDPGPPGAPG IPGPKGDIGE KGDSGPSGAA GPPGKKGPPG EDGAKGSVGP
TGLPGDLGPP GDPGVSGIDG SPGEKGDPGD VGGPGPPGAS GEPGAPGPPG KRGPSGHMGR
EGREGEKGAK GEPGPDGPPG RTGPMGARGP PGRVGPEGLR GIPGPVGEPG LLGAPGQMGP
PGPLGPSGLP GLKGDTGPKG EKGHIGLIGL IGPPGEAGEK GDQGLPGVQG PPGPKGDPGP
PGPIGSLGHP GPPGVAGPLG QKGSKGSPGS MGPRGDTGPA GPPGPPGPPA ELHGLRRRRR
FVPVPLPVVE GGLEEVLASL TSLSLELEQL RRPPGTAERP GLVCHELHRN HPHLPDGEYW
IDPNQGCARD SFRVFCNFTA GGETCLYPDK KFEIVKLASW SKEKPGGWYS TFRRGKKFSY
VDADGSPVNV VQLNFLKLLS ATARQNFTYS CQNAAAWLDE ATGDYSHSAR FLGTNGEELS
FNQTTAATVS VPQDGCRLRK GQTKTLFEFS SSRAGFLPLW DVAATDFGQT NQKFGFELGP
VCFSS*
speed 1.27 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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