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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000272367
Querying Taster for transcript #2: ENST00000426626
MT speed 2.33 s - this script 8.42021 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CLEC4Fpolymorphism_automatic9.99200722162641e-16simple_aaeaffectedK564Rsingle base exchangers2287101show file
CLEC4Fpolymorphism_automatic9.89824200381406e-08without_aaeaffectedsingle base exchangers2287101show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999999 (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) chr2:71036482T>CN/A show variant in all transcripts   IGV
HGNC symbol CLEC4F
Ensembl transcript ID ENST00000272367
Genbank transcript ID NM_173535
UniProt peptide Q8N1N0
alteration type single base exchange
alteration region CDS
DNA changes c.1691A>G
cDNA.1768A>G
g.11251A>G
AA changes K564R Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS
564
frameshift no
known variant Reference ID: rs2287101
databasehomozygous (C/C)heterozygousallele carriers
1000G135645780
ExAC1059943410493
regulatory features H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1480
-0.0580
(flanking)0.0050
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained112450.95mu: CCCACTCAGAAGGTA CACT|caga
Donor gained112500.86mu: TCAGAAGGTATATTA AGAA|ggta
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      564APGSKGSCPLRKYIIVNSGMGACS
mutated  all conserved    564APGSKGSCPLRRYIIVNSGMGAC
Ptroglodytes  all conserved  ENSPTRG00000012035  513APGSKGSCPLRRYISVNSGMGAC
Mmulatta  all conserved  ENSMMUG00000020854  560TPGSKGPCPLRRHISVNSGVGAC
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000014542  n/a
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
61589TOPO_DOMExtracellular (Potential).lost
476589DOMAINC-type lectin.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1770 / 1770
position (AA) of stopcodon in wt / mu AA sequence 590 / 590
position of stopcodon in wt / mu cDNA 1847 / 1847
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 78 / 78
chromosome 2
strand -1
last intron/exon boundary 1736
theoretical NMD boundary in CDS 1608
length of CDS 1770
coding sequence (CDS) position 1691
cDNA position
(for ins/del: last normal base / first normal base)
1768
gDNA position
(for ins/del: last normal base / first normal base)
11251
chromosomal position
(for ins/del: last normal base / first normal base)
71036482
original gDNA sequence snippet GGGATCCTGCCCACTCAGAAAGTATATTATTGTGAATTCTG
altered gDNA sequence snippet GGGATCCTGCCCACTCAGAAGGTATATTATTGTGAATTCTG
original cDNA sequence snippet GGGATCCTGCCCACTCAGAAAGTATATTATTGTGAATTCTG
altered cDNA sequence snippet GGGATCCTGCCCACTCAGAAGGTATATTATTGTGAATTCTG
wildtype AA sequence MDGEAVRFCT DNQCVSLHPQ EVDSVAMAPA APKIPRLVQA TPAFMAVTLV FSLVTLFVVV
QQQTRPVPKP VQAVILGDNI TGHLPFEPNN HHHFGREAEM RELIQTFKGH MENSSAWVVE
IQMLKCRVDN VNSQLQVLGD HLGNTNADIQ MVKGVLKDAT TLSLQTQMLR SSLEGTNAEI
QRLKEDLEKA DALTFQTLNF LKSSLENTSI ELHVLSRGLE NANSEIQMLN ASLETANTQA
QLANSSLKNA NAEIYVLRGH LDSVNDLRTQ NQVLRNSLEG ANAEIQGLKE NLQNTNALNS
QTQAFIKSSF DNTSAEIQFL RGHLERAGDE IHVLKRDLKM VTAQTQKANG RLDQTDTQIQ
VFKSEMENVN TLNAQIQVLN GHMKNASREI QTLKQGMKNA SALTSQTQML DSNLQKASAE
IQRLRGDLEN TKALTMEIQQ EQSRLKTLHV VITSQEQLQR TQSQLLQMVL QGWKFNGGSL
YYFSSVKKSW HEAEQFCVSQ GAHLASVASK EEQAFLVEFT SKVYYWIGLT DRGTEGSWRW
TDGTPFNAAQ NKAPGSKGSC PLRKYIIVNS GMGACSFIDT PPCPWILSN*
mutated AA sequence MDGEAVRFCT DNQCVSLHPQ EVDSVAMAPA APKIPRLVQA TPAFMAVTLV FSLVTLFVVV
QQQTRPVPKP VQAVILGDNI TGHLPFEPNN HHHFGREAEM RELIQTFKGH MENSSAWVVE
IQMLKCRVDN VNSQLQVLGD HLGNTNADIQ MVKGVLKDAT TLSLQTQMLR SSLEGTNAEI
QRLKEDLEKA DALTFQTLNF LKSSLENTSI ELHVLSRGLE NANSEIQMLN ASLETANTQA
QLANSSLKNA NAEIYVLRGH LDSVNDLRTQ NQVLRNSLEG ANAEIQGLKE NLQNTNALNS
QTQAFIKSSF DNTSAEIQFL RGHLERAGDE IHVLKRDLKM VTAQTQKANG RLDQTDTQIQ
VFKSEMENVN TLNAQIQVLN GHMKNASREI QTLKQGMKNA SALTSQTQML DSNLQKASAE
IQRLRGDLEN TKALTMEIQQ EQSRLKTLHV VITSQEQLQR TQSQLLQMVL QGWKFNGGSL
YYFSSVKKSW HEAEQFCVSQ GAHLASVASK EEQAFLVEFT SKVYYWIGLT DRGTEGSWRW
TDGTPFNAAQ NKAPGSKGSC PLRRYIIVNS GMGACSFIDT PPCPWILSN*
speed 1.58 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: without_aae, prob: 0.99999990101758 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr2:71036482T>CN/A show variant in all transcripts   IGV
HGNC symbol CLEC4F
Ensembl transcript ID ENST00000426626
Genbank transcript ID N/A
UniProt peptide Q8N1N0
alteration type single base exchange
alteration region intron
DNA changes g.11251A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs2287101
databasehomozygous (C/C)heterozygousallele carriers
1000G135645780
ExAC1059943410493
regulatory features H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1480
-0.0580
(flanking)0.0050
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained112450.95mu: CCCACTCAGAAGGTA CACT|caga
Donor gained112500.86mu: TCAGAAGGTATATTA AGAA|ggta
distance from splice site 208
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
61589TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
476589DOMAINC-type lectin.might get lost (downstream of altered splice site)
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 25 / 25
chromosome 2
strand -1
last intron/exon boundary 1683
theoretical NMD boundary in CDS 1608
length of CDS 1704
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)
11251
chromosomal position
(for ins/del: last normal base / first normal base)
71036482
original gDNA sequence snippet GGGATCCTGCCCACTCAGAAAGTATATTATTGTGAATTCTG
altered gDNA sequence snippet GGGATCCTGCCCACTCAGAAGGTATATTATTGTGAATTCTG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDGEAVRFCT DNQCVSLHPQ EVDSVAMAPA APKIPRLVQA TPAFMAVTLV FSLVTLFVVV
QQQTRPVPKP VQAVILGDNI TGHLPFEPNN HHHFGREAEM RELIQTFKGH MENSSAWVVE
IQMLKCRVDN VNSQLQVLGD HLGNTNADIQ MVKGVLKDAT TLSLQTQMLR SSLEGTNAEI
QRLKEDLEKA DALTFQTLNF LKSSLENTSI ELHVLSRGLE NANSEIQMLN ASLETANTQA
QLANSSLKNA NAEIYVLRGH LDSVNDLRTQ NQVLRNSLEG ANAEIQGLKE NLQNTNALNS
QTQAFIKSSF DNTSAEIQFL RGHLERAGDE IHVLKRDLKM VTAQTQKANG RLDQTDTQIQ
VFKSEMENVN TLNAQIQVLN GHMKNASREI QTLKQGMKNA SALTSQTQML DSNLQKASAE
IQRLRGDLEN TKALTMEIQQ EQSRLKTLHV VITSQEQLQR TQSQLLQMVL QGWKFNGGSL
YYFSSVKKSW HEAEQFCVSQ GAHLASVASK EEQAFLVEFT SKVYYWIGLT DRGTEGSWRW
TDGTPFNAAQ NKASHSTRKG CCLHLTV*
mutated AA sequence N/A
speed 0.75 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