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: ENST00000355690
Querying Taster for transcript #2: ENST00000304361
Querying Taster for transcript #3: ENST00000350667
MT speed 1.69 s - this script 3.077591 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CLEC12Apolymorphism_automatic5.99520433297585e-15simple_aaeaffectedK254Qsingle base exchangers479499show file
CLEC12Apolymorphism_automatic9.99200722162641e-15simple_aaeaffectedK244Qsingle base exchangers479499show file
CLEC12Apolymorphism_automatic9.99200722162641e-15simple_aaeaffectedK211Qsingle base exchangers479499show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999994 (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) chr12:10137557A>CN/A show variant in all transcripts   IGV
HGNC symbol CLEC12A
Ensembl transcript ID ENST00000355690
Genbank transcript ID NM_001207010
UniProt peptide Q5QGZ9
alteration type single base exchange
alteration region CDS
DNA changes c.760A>C
cDNA.791A>C
g.33643A>C
AA changes K254Q Score: 53 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 254
frameshift no
known variant Reference ID: rs479499
databasehomozygous (C/C)heterozygousallele carriers
1000G13849252309
ExAC14239428918528
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.2940
-1.9990
(flanking)-0.1590
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased33637wt: 0.21 / mu: 0.29wt: TTCAATATTATCACTGCACTTATAAAAAAAGAATGATATGT
mu: TTCAATATTATCACTGCACTTATAAACAAAGAATGATATGT		 actt|ATAA
Acc increased33641wt: 0.28 / mu: 0.36wt: ATATTATCACTGCACTTATAAAAAAAGAATGATATGTGAGA
mu: ATATTATCACTGCACTTATAAACAAAGAATGATATGTGAGA		 ataa|AAAA
Acc increased33635wt: 0.26 / mu: 0.40wt: TGTTCAATATTATCACTGCACTTATAAAAAAAGAATGATAT
mu: TGTTCAATATTATCACTGCACTTATAAACAAAGAATGATAT		 gcac|TTAT
Donor increased33645wt: 0.51 / mu: 0.59wt: AAAAAAAGAATGATA
mu: AAACAAAGAATGATA		 AAAA|agaa
distance from splice site 89
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      254LYVQYYHCTYKKRMICEKMANPVQ
mutated  all conserved    254LYVQYYHCTYKQRMICEKMANPV
Ptroglodytes  all conserved  ENSPTRG00000039976  254LYVQYYHCTYKQRMICEKMANPV
Mmulatta  all identical  ENSMMUG00000002956  244IYRKKMICEKMANPV
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000053063  242TDENNIICEETASKV
Ggallus  all conserved  ENSGALG00000014722  221IIYASNSCSTKQSWICEKGA
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
65265TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 828 / 828
position (AA) of stopcodon in wt / mu AA sequence 276 / 276
position of stopcodon in wt / mu cDNA 859 / 859
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 32 / 32
chromosome 12
strand 1
last intron/exon boundary 703
theoretical NMD boundary in CDS 621
length of CDS 828
coding sequence (CDS) position 760
cDNA position
(for ins/del: last normal base / first normal base)		 791
gDNA position
(for ins/del: last normal base / first normal base)		 33643
chromosomal position
(for ins/del: last normal base / first normal base)		 10137557
original gDNA sequence snippet ATTATCACTGCACTTATAAAAAAAGAATGATATGTGAGAAG
altered gDNA sequence snippet ATTATCACTGCACTTATAAACAAAGAATGATATGTGAGAAG
original cDNA sequence snippet ATTATCACTGCACTTATAAAAAAAGAATGATATGTGAGAAG
altered cDNA sequence snippet ATTATCACTGCACTTATAAACAAAGAATGATATGTGAGAAG
wildtype AA sequence MWIDFFTYSS MSEEVTYADL QFQNSSEMEK IPEIGKFGEK APPAPSHVWR PAALFLTLLC
LLLLIGLGVL ASMFHVTLKI EMKKMNKLQN ISEELQRNIS LQLMSNMNIS NKIRNLSTTL
QTIATKLCRE LYSKEQEHKC KPCPRRWIWH KDSCYFLSDD VQTWQESKMA CAAQNASLLK
INNKNALEFI KSQSRSYDYW LGLSPEEDST RGMRVDNIIN SSAWVIRNAP DLNNMYCGYI
NRLYVQYYHC TYKKRMICEK MANPVQLGST YFREA*
mutated AA sequence MWIDFFTYSS MSEEVTYADL QFQNSSEMEK IPEIGKFGEK APPAPSHVWR PAALFLTLLC
LLLLIGLGVL ASMFHVTLKI EMKKMNKLQN ISEELQRNIS LQLMSNMNIS NKIRNLSTTL
QTIATKLCRE LYSKEQEHKC KPCPRRWIWH KDSCYFLSDD VQTWQESKMA CAAQNASLLK
INNKNALEFI KSQSRSYDYW LGLSPEEDST RGMRVDNIIN SSAWVIRNAP DLNNMYCGYI
NRLYVQYYHC TYKQRMICEK MANPVQLGST YFREA*
speed 0.68 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: 0.99999999999999 (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) chr12:10137557A>CN/A show variant in all transcripts   IGV
HGNC symbol CLEC12A
Ensembl transcript ID ENST00000304361
Genbank transcript ID NM_138337
UniProt peptide Q5QGZ9
alteration type single base exchange
alteration region CDS
DNA changes c.730A>C
cDNA.912A>C
g.33643A>C
AA changes K244Q Score: 53 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 244
frameshift no
known variant Reference ID: rs479499
databasehomozygous (C/C)heterozygousallele carriers
1000G13849252309
ExAC14239428918528
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.2940
-1.9990
(flanking)-0.1590
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased33637wt: 0.21 / mu: 0.29wt: TTCAATATTATCACTGCACTTATAAAAAAAGAATGATATGT
mu: TTCAATATTATCACTGCACTTATAAACAAAGAATGATATGT		 actt|ATAA
Acc increased33641wt: 0.28 / mu: 0.36wt: ATATTATCACTGCACTTATAAAAAAAGAATGATATGTGAGA
mu: ATATTATCACTGCACTTATAAACAAAGAATGATATGTGAGA		 ataa|AAAA
Acc increased33635wt: 0.26 / mu: 0.40wt: TGTTCAATATTATCACTGCACTTATAAAAAAAGAATGATAT
mu: TGTTCAATATTATCACTGCACTTATAAACAAAGAATGATAT		 gcac|TTAT
Donor increased33645wt: 0.51 / mu: 0.59wt: AAAAAAAGAATGATA
mu: AAACAAAGAATGATA		 AAAA|agaa
distance from splice site 89
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      244LYVQYYHCTYKKRMICEKMANPVQ
mutated  all conserved    244TYKQRMICEKMANPV
Ptroglodytes  all conserved  ENSPTRG00000039976  254TYKQRMICEKMANPV
Mmulatta  all identical  ENSMMUG00000002956  244IYRKKMICEKMANPV
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000053063  242TDENNIICEETASKV
Ggallus  all conserved  ENSGALG00000014722  221IIYASNSCSTKQSWICEKGA
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
65265TOPO_DOMExtracellular (Potential).lost
140249DOMAINC-type lectin.lost
240240DISULFIDBy similarity.might get lost (downstream of altered splice site)
248248DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 798 / 798
position (AA) of stopcodon in wt / mu AA sequence 266 / 266
position of stopcodon in wt / mu cDNA 980 / 980
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 183 / 183
chromosome 12
strand 1
last intron/exon boundary 824
theoretical NMD boundary in CDS 591
length of CDS 798
coding sequence (CDS) position 730
cDNA position
(for ins/del: last normal base / first normal base)		 912
gDNA position
(for ins/del: last normal base / first normal base)		 33643
chromosomal position
(for ins/del: last normal base / first normal base)		 10137557
original gDNA sequence snippet ATTATCACTGCACTTATAAAAAAAGAATGATATGTGAGAAG
altered gDNA sequence snippet ATTATCACTGCACTTATAAACAAAGAATGATATGTGAGAAG
original cDNA sequence snippet ATTATCACTGCACTTATAAAAAAAGAATGATATGTGAGAAG
altered cDNA sequence snippet ATTATCACTGCACTTATAAACAAAGAATGATATGTGAGAAG
wildtype AA sequence MSEEVTYADL QFQNSSEMEK IPEIGKFGEK APPAPSHVWR PAALFLTLLC LLLLIGLGVL
ASMFHVTLKI EMKKMNKLQN ISEELQRNIS LQLMSNMNIS NKIRNLSTTL QTIATKLCRE
LYSKEQEHKC KPCPRRWIWH KDSCYFLSDD VQTWQESKMA CAAQNASLLK INNKNALEFI
KSQSRSYDYW LGLSPEEDST RGMRVDNIIN SSAWVIRNAP DLNNMYCGYI NRLYVQYYHC
TYKKRMICEK MANPVQLGST YFREA*
mutated AA sequence MSEEVTYADL QFQNSSEMEK IPEIGKFGEK APPAPSHVWR PAALFLTLLC LLLLIGLGVL
ASMFHVTLKI EMKKMNKLQN ISEELQRNIS LQLMSNMNIS NKIRNLSTTL QTIATKLCRE
LYSKEQEHKC KPCPRRWIWH KDSCYFLSDD VQTWQESKMA CAAQNASLLK INNKNALEFI
KSQSRSYDYW LGLSPEEDST RGMRVDNIIN SSAWVIRNAP DLNNMYCGYI NRLYVQYYHC
TYKQRMICEK MANPVQLGST YFREA*
speed 0.68 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: 0.99999999999999 (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) chr12:10137557A>CN/A show variant in all transcripts   IGV
HGNC symbol CLEC12A
Ensembl transcript ID ENST00000350667
Genbank transcript ID NM_201623
UniProt peptide Q5QGZ9
alteration type single base exchange
alteration region CDS
DNA changes c.631A>C
cDNA.631A>C
g.33643A>C
AA changes K211Q Score: 53 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 211
frameshift no
known variant Reference ID: rs479499
databasehomozygous (C/C)heterozygousallele carriers
1000G13849252309
ExAC14239428918528
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.2940
-1.9990
(flanking)-0.1590
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased33637wt: 0.21 / mu: 0.29wt: TTCAATATTATCACTGCACTTATAAAAAAAGAATGATATGT
mu: TTCAATATTATCACTGCACTTATAAACAAAGAATGATATGT		 actt|ATAA
Acc increased33641wt: 0.28 / mu: 0.36wt: ATATTATCACTGCACTTATAAAAAAAGAATGATATGTGAGA
mu: ATATTATCACTGCACTTATAAACAAAGAATGATATGTGAGA		 ataa|AAAA
Acc increased33635wt: 0.26 / mu: 0.40wt: TGTTCAATATTATCACTGCACTTATAAAAAAAGAATGATAT
mu: TGTTCAATATTATCACTGCACTTATAAACAAAGAATGATAT		 gcac|TTAT
Donor increased33645wt: 0.51 / mu: 0.59wt: AAAAAAAGAATGATA
mu: AAACAAAGAATGATA		 AAAA|agaa
distance from splice site 69
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      211LYVQYYHCTYKKRMICEKMANPVQ
mutated  all conserved    211LYVQYYHCTYKQRMICEKMANPV
Ptroglodytes  all conserved  ENSPTRG00000039976  254TYKQRMICEKMANPV
Mmulatta  all identical  ENSMMUG00000002956  244IYRKKMICEKMANPV
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000053063  242TDENNIICEETASKV
Ggallus  all conserved  ENSGALG00000014722  220IIYASNSCSTKQSWICEKGA
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
65265TOPO_DOMExtracellular (Potential).lost
140249DOMAINC-type lectin.lost
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
240240DISULFIDBy similarity.might get lost (downstream of altered splice site)
248248DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 699 / 699
position (AA) of stopcodon in wt / mu AA sequence 233 / 233
position of stopcodon in wt / mu cDNA 699 / 699
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 1 / 1
chromosome 12
strand 1
last intron/exon boundary 543
theoretical NMD boundary in CDS 492
length of CDS 699
coding sequence (CDS) position 631
cDNA position
(for ins/del: last normal base / first normal base)		 631
gDNA position
(for ins/del: last normal base / first normal base)		 33643
chromosomal position
(for ins/del: last normal base / first normal base)		 10137557
original gDNA sequence snippet ATTATCACTGCACTTATAAAAAAAGAATGATATGTGAGAAG
altered gDNA sequence snippet ATTATCACTGCACTTATAAACAAAGAATGATATGTGAGAAG
original cDNA sequence snippet ATTATCACTGCACTTATAAAAAAAGAATGATATGTGAGAAG
altered cDNA sequence snippet ATTATCACTGCACTTATAAACAAAGAATGATATGTGAGAAG
wildtype AA sequence MSEEVTYADL QFQNSSEMEK IPEIGKFGEK VHVTLKIEMK KMNKLQNISE ELQRNISLQL
MSNMNISNKI RNLSTTLQTI ATKLCRELYS KEQEHKCKPC PRRWIWHKDS CYFLSDDVQT
WQESKMACAA QNASLLKINN KNALEFIKSQ SRSYDYWLGL SPEEDSTRGM RVDNIINSSA
WVIRNAPDLN NMYCGYINRL YVQYYHCTYK KRMICEKMAN PVQLGSTYFR EA*
mutated AA sequence MSEEVTYADL QFQNSSEMEK IPEIGKFGEK VHVTLKIEMK KMNKLQNISE ELQRNISLQL
MSNMNISNKI RNLSTTLQTI ATKLCRELYS KEQEHKCKPC PRRWIWHKDS CYFLSDDVQT
WQESKMACAA QNASLLKINN KNALEFIKSQ SRSYDYWLGL SPEEDSTRGM RVDNIINSSA
WVIRNAPDLN NMYCGYINRL YVQYYHCTYK QRMICEKMAN PVQLGSTYFR EA*
speed 0.33 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