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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: ENST00000381624
MT speed 1.54 s - this script 6.090256 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CATSPERDpolymorphism_automatic4.09694500547175e-12simple_aaeaffectedG639Rsingle base exchangers61180947show file

Taster files

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999995903 (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) chr19:5772950G>AN/A show variant in all transcripts   IGV
HGNC symbol CATSPERD
Ensembl transcript ID ENST00000381624
Genbank transcript ID NM_152784
UniProt peptide Q86XM0
alteration type single base exchange
alteration region CDS
DNA changes c.1915G>A
cDNA.1976G>A
g.52263G>A
AA changes G639R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS
639
frameshift no
known variant Reference ID: rs61180947
databasehomozygous (A/A)heterozygousallele carriers
1000G188774962
ExAC48872111526002
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-6.5980
0.6720.001
(flanking)0.2030
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased52255wt: 0.7868 / mu: 0.8010 (marginal change - not scored)wt: GATAAAGGAATTCGG
mu: GATAAAGGAATTCAG
 TAAA|ggaa
Donor gained522590.31mu: AAGGAATTCAGGGGG GGAA|ttca
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      639PQNWTTMIKEFGGPFFWNRENYVS
mutated  not conserved    639PQNWTTMIKEFRGPFFWNRENYV
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000040828  636PQNWSTFESDIENEEPFLWNRENYV
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 
21718TOPO_DOMExtracellular (Potential).lost
719739TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
740798TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2397 / 2397
position (AA) of stopcodon in wt / mu AA sequence 799 / 799
position of stopcodon in wt / mu cDNA 2458 / 2458
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 62 / 62
chromosome 19
strand 1
last intron/exon boundary 2158
theoretical NMD boundary in CDS 2046
length of CDS 2397
coding sequence (CDS) position 1915
cDNA position
(for ins/del: last normal base / first normal base)
1976
gDNA position
(for ins/del: last normal base / first normal base)
52263
chromosomal position
(for ins/del: last normal base / first normal base)
5772950
original gDNA sequence snippet CCACCATGATAAAGGAATTCGGGGGGCCCTTCTTCTGGAAC
altered gDNA sequence snippet CCACCATGATAAAGGAATTCAGGGGGCCCTTCTTCTGGAAC
original cDNA sequence snippet CCACCATGATAAAGGAATTCGGGGGGCCCTTCTTCTGGAAC
altered cDNA sequence snippet CCACCATGATAAAGGAATTCAGGGGGCCCTTCTTCTGGAAC
wildtype AA sequence MLMLMLVAAV TMWLRPLVTA QLCRSRTVRT GKVFNLIQDV QGDRLYFHPT TTRLIKHPCE
KNIALYLGKQ VFFTMDNFET SLLPFTIPTS MQVGVPEVTS AHFAGSLLLL VVDQKVYIYD
YENNSWSMSL GIKHPVTHVS GDNCCYTGSL FCVHVSNLVF AYFRGDQISQ TYIYYSNTGG
FSFWKYHYDR QAEIIGSLGG IFHFFSLSQV AMLVVNQGKG MFKYSDHPLN RSFGLSFDYN
GTLDILIAPG QRGILLLWFE NSLLFSHNAG QLVDTVRVKK GDQTLFSSIF EAKITIHNIA
VTENELAVIT REDNLYYGNL GIVPSSIIKF ADQYIWSEDV ALMFRSPGTL EILTPLRDTA
FPAFDFQKCL VNIQALLMDP ELHVGKCKIE FLTGEFIYRM YTIDMHSQLE LTASLIPQPG
TSLIPLVMVS NPHSLGFQAT FYENGYTSDG NTKYKLDIFL KQQQHWGRTD SNFTSSLKKA
TMSTLTVDIA NKEISCVDIK PLSTLISVGC DLDKKIVIQN KVSACSMGIL DPLTLQDNYS
FIIEKEFYDP GFQGQQSSED LHVFYSYQQL GCPLLVYYDT LWKPVVELWR KDSFQEVIDA
EYVLLEVNGQ FSYSYSLTAQ SAMCTSQPQN WTTMIKEFGG PFFWNRENYV SCHDPNNNAP
LRWPDVQYQI LGGRTANQII FGHNGFYVFY ISIVDPYYSY CQLETIFSIY VYGAFPVQLV
SAGVVILLII SSILGSVWLA YKTPKLLRTA RGRRIKKCAT QLCRRCKTVC QFRASATARA
GTEPPGRHRT PHGGRSDH*
mutated AA sequence MLMLMLVAAV TMWLRPLVTA QLCRSRTVRT GKVFNLIQDV QGDRLYFHPT TTRLIKHPCE
KNIALYLGKQ VFFTMDNFET SLLPFTIPTS MQVGVPEVTS AHFAGSLLLL VVDQKVYIYD
YENNSWSMSL GIKHPVTHVS GDNCCYTGSL FCVHVSNLVF AYFRGDQISQ TYIYYSNTGG
FSFWKYHYDR QAEIIGSLGG IFHFFSLSQV AMLVVNQGKG MFKYSDHPLN RSFGLSFDYN
GTLDILIAPG QRGILLLWFE NSLLFSHNAG QLVDTVRVKK GDQTLFSSIF EAKITIHNIA
VTENELAVIT REDNLYYGNL GIVPSSIIKF ADQYIWSEDV ALMFRSPGTL EILTPLRDTA
FPAFDFQKCL VNIQALLMDP ELHVGKCKIE FLTGEFIYRM YTIDMHSQLE LTASLIPQPG
TSLIPLVMVS NPHSLGFQAT FYENGYTSDG NTKYKLDIFL KQQQHWGRTD SNFTSSLKKA
TMSTLTVDIA NKEISCVDIK PLSTLISVGC DLDKKIVIQN KVSACSMGIL DPLTLQDNYS
FIIEKEFYDP GFQGQQSSED LHVFYSYQQL GCPLLVYYDT LWKPVVELWR KDSFQEVIDA
EYVLLEVNGQ FSYSYSLTAQ SAMCTSQPQN WTTMIKEFRG PFFWNRENYV SCHDPNNNAP
LRWPDVQYQI LGGRTANQII FGHNGFYVFY ISIVDPYYSY CQLETIFSIY VYGAFPVQLV
SAGVVILLII SSILGSVWLA YKTPKLLRTA RGRRIKKCAT QLCRRCKTVC QFRASATARA
GTEPPGRHRT PHGGRSDH*
speed 1.54 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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