Yum, tasty mutations...

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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000533902
Querying Taster for transcript #2: ENST00000531380
MT speed 0 s - this script 3.190507 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FZD4disease_causing_automatic0.999999959004218simple_aae0M105Vsingle base exchangers80358284show file
PRSS23disease_causing_automatic1without_aaeaffected0single base exchangers80358284show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999959004218 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032569)
  • known disease mutation: rs224624 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:86663485T>CN/A show variant in all transcripts   IGV
HGNC symbol FZD4
Ensembl transcript ID ENST00000531380
Genbank transcript ID NM_012193
UniProt peptide Q9ULV1
alteration type single base exchange
alteration region CDS
DNA changes c.313A>G
cDNA.619A>G
g.2949A>G
AA changes M105V Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 105
frameshift no
known variant Reference ID: rs80358284
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs224624 (pathogenic for Retinal dystrophy|Exudative retinopathy|Familial exudative vitreoretinopathy|Exudative vitreoretinopathy 1|Atrophia bulborum hereditaria|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032569)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032569)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032569)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1611
3.6371
(flanking)-0.6780.881
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 increased2940wt: 0.9921 / mu: 0.9928 (marginal change - not scored)wt: AGTTCTTCCTTTGTTCTGTTTATGTGCCAATGTGCACAGAG
mu: AGTTCTTCCTTTGTTCTGTTTATGTGCCAGTGTGCACAGAG		 gttt|ATGT
Acc marginally increased2943wt: 0.5073 / mu: 0.5349 (marginal change - not scored)wt: TCTTCCTTTGTTCTGTTTATGTGCCAATGTGCACAGAGAAG
mu: TCTTCCTTTGTTCTGTTTATGTGCCAGTGTGCACAGAGAAG		 tatg|TGCC
Acc marginally increased2941wt: 0.9615 / mu: 0.9756 (marginal change - not scored)wt: GTTCTTCCTTTGTTCTGTTTATGTGCCAATGTGCACAGAGA
mu: GTTCTTCCTTTGTTCTGTTTATGTGCCAGTGTGCACAGAGA		 ttta|TGTG
Acc marginally increased2942wt: 0.9970 / mu: 0.9975 (marginal change - not scored)wt: TTCTTCCTTTGTTCTGTTTATGTGCCAATGTGCACAGAGAA
mu: TTCTTCCTTTGTTCTGTTTATGTGCCAGTGTGCACAGAGAA		 ttat|GTGC
Acc marginally increased2946wt: 0.7720 / mu: 0.7748 (marginal change - not scored)wt: TCCTTTGTTCTGTTTATGTGCCAATGTGCACAGAGAAGATC
mu: TCCTTTGTTCTGTTTATGTGCCAGTGTGCACAGAGAAGATC		 gtgc|CAAT
Acc marginally increased2948wt: 0.9300 / mu: 0.9817 (marginal change - not scored)wt: CTTTGTTCTGTTTATGTGCCAATGTGCACAGAGAAGATCAA
mu: CTTTGTTCTGTTTATGTGCCAGTGTGCACAGAGAAGATCAA		 gcca|ATGT
distance from splice site 28
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      105LQFFLCSVYVPMCTEKINIPIGPC
mutated  all conserved    105LQFFLCSVYVPVCTEKINIPIGP
Ptroglodytes  all identical  ENSPTRG00000004148  105LQFFLCSVYVPMCTEKINIPIGP
Mmulatta  all identical  ENSMMUG00000004048  105LQFFLCSVYVPMCTEKINIPIGP
Fcatus  all identical  ENSFCAG00000011826  108LQFFLCSVYVPMCTEKINIPIGP
Mmusculus  all identical  ENSMUSG00000049791  105LQFFLCSVYVPMCTEKINIPIGP
Ggallus  all identical  ENSGALG00000017242  93LQFFLCSVYVPMCTEKINIPIGP
Trubripes  all identical  ENSTRUG00000006345  97LKFFLCSVYVPMCTVKIPIPIGP
Drerio  all identical  ENSDARG00000077111  91LKFFLCSVYVPMCTEKVPIPIGP
Dmelanogaster  all conserved  FBgn0016797  124LKFFLCSMYTPICLEDYHKPLPV
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000010434  91LQFFLCSVYVPMCTEKINIPIGP
protein features
start (aa)end (aa)featuredetails 
37222TOPO_DOMExtracellular (Potential).lost
40161DOMAINFZ.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1614 / 1614
position (AA) of stopcodon in wt / mu AA sequence 538 / 538
position of stopcodon in wt / mu cDNA 1920 / 1920
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 307 / 307
chromosome 11
strand -1
last intron/exon boundary 592
theoretical NMD boundary in CDS 235
length of CDS 1614
coding sequence (CDS) position 313
cDNA position
(for ins/del: last normal base / first normal base)		 619
gDNA position
(for ins/del: last normal base / first normal base)		 2949
chromosomal position
(for ins/del: last normal base / first normal base)		 86663485
original gDNA sequence snippet TTTGTTCTGTTTATGTGCCAATGTGCACAGAGAAGATCAAC
altered gDNA sequence snippet TTTGTTCTGTTTATGTGCCAGTGTGCACAGAGAAGATCAAC
original cDNA sequence snippet TTTGTTCTGTTTATGTGCCAATGTGCACAGAGAAGATCAAC
altered cDNA sequence snippet TTTGTTCTGTTTATGTGCCAGTGTGCACAGAGAAGATCAAC
wildtype AA sequence MAWRGAGPSV PGAPGGVGLS LGLLLQLLLL LGPARGFGDE EERRCDPIRI SMCQNLGYNV
TKMPNLVGHE LQTDAELQLT TFTPLIQYGC SSQLQFFLCS VYVPMCTEKI NIPIGPCGGM
CLSVKRRCEP VLKEFGFAWP ESLNCSKFPP QNDHNHMCME GPGDEEVPLP HKTPIQPGEE
CHSVGTNSDQ YIWVKRSLNC VLKCGYDAGL YSRSAKEFTD IWMAVWASLC FISTAFTVLT
FLIDSSRFSY PERPIIFLSM CYNIYSIAYI VRLTVGRERI SCDFEEAAEP VLIQEGLKNT
GCAIIFLLMY FFGMASSIWW VILTLTWFLA AGLKWGHEAI EMHSSYFHIA AWAIPAVKTI
VILIMRLVDA DELTGLCYVG NQNLDALTGF VVAPLFTYLV IGTLFIAAGL VALFKIRSNL
QKDGTKTDKL ERLMVKIGVF SVLYTVPATC VIACYFYEIS NWALFRYSAD DSNMAVEMLK
IFMSLLVGIT SGMWIWSAKT LHTWQKCSNR LVNSGKVKRE KRGNGWVKPG KGSETVV*
mutated AA sequence MAWRGAGPSV PGAPGGVGLS LGLLLQLLLL LGPARGFGDE EERRCDPIRI SMCQNLGYNV
TKMPNLVGHE LQTDAELQLT TFTPLIQYGC SSQLQFFLCS VYVPVCTEKI NIPIGPCGGM
CLSVKRRCEP VLKEFGFAWP ESLNCSKFPP QNDHNHMCME GPGDEEVPLP HKTPIQPGEE
CHSVGTNSDQ YIWVKRSLNC VLKCGYDAGL YSRSAKEFTD IWMAVWASLC FISTAFTVLT
FLIDSSRFSY PERPIIFLSM CYNIYSIAYI VRLTVGRERI SCDFEEAAEP VLIQEGLKNT
GCAIIFLLMY FFGMASSIWW VILTLTWFLA AGLKWGHEAI EMHSSYFHIA AWAIPAVKTI
VILIMRLVDA DELTGLCYVG NQNLDALTGF VVAPLFTYLV IGTLFIAAGL VALFKIRSNL
QKDGTKTDKL ERLMVKIGVF SVLYTVPATC VIACYFYEIS NWALFRYSAD DSNMAVEMLK
IFMSLLVGIT SGMWIWSAKT LHTWQKCSNR LVNSGKVKRE KRGNGWVKPG KGSETVV*
speed 0.46 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

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 CM032569)
  • known disease mutation: rs224624 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:86663485T>CN/A show variant in all transcripts   IGV
HGNC symbol PRSS23
Ensembl transcript ID ENST00000533902
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region 3'UTR
DNA changes cDNA.1576T>C
g.161385T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs80358284
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs224624 (pathogenic for Retinal dystrophy|Exudative retinopathy|Familial exudative vitreoretinopathy|Exudative vitreoretinopathy 1|Atrophia bulborum hereditaria|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032569)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032569)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032569)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1611
3.6371
(flanking)-0.6780.881
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change occurs after stopcodon (at aa 475)
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased161379wt: 0.9211 / mu: 0.9417 (marginal change - not scored)wt: GGGGATGTTGATCTTCTCTGTGCACATTGGCACATAAACAG
mu: GGGGATGTTGATCTTCTCTGTGCACACTGGCACATAAACAG		 ctgt|GCAC
Acc increased161377wt: 0.45 / mu: 0.57wt: ATGGGGATGTTGATCTTCTCTGTGCACATTGGCACATAAAC
mu: ATGGGGATGTTGATCTTCTCTGTGCACACTGGCACATAAAC		 ctct|GTGC
distance from splice site 402
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 signal is predicted to be ok
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 143 / 143
chromosome 11
strand 1
last intron/exon boundary 349
theoretical NMD boundary in CDS 156
length of CDS 276
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 1576
gDNA position
(for ins/del: last normal base / first normal base)		 161385
chromosomal position
(for ins/del: last normal base / first normal base)		 86663485
original gDNA sequence snippet GTTGATCTTCTCTGTGCACATTGGCACATAAACAGAACAAA
altered gDNA sequence snippet GTTGATCTTCTCTGTGCACACTGGCACATAAACAGAACAAA
original cDNA sequence snippet GTTGATCTTCTCTGTGCACATTGGCACATAAACAGAACAAA
altered cDNA sequence snippet GTTGATCTTCTCTGTGCACACTGGCACATAAACAGAACAAA
wildtype AA sequence MSRMRPVCQP WPSPHAPTTV KREGSTVSNS IQPPPPEYQL GSRTWLEAET PGQKRQCSAF
MEFTEESRRI HQSVGTLLPR VKSFGRPNPH A*
mutated AA sequence N/A
speed 0.78 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

Problems