Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999933899 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042690)
  • known disease mutation: rs65657 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:68560809G>AN/A show variant in all transcripts   IGV
HGNC symbol CPT1A
Ensembl transcript ID ENST00000538994
Genbank transcript ID N/A
UniProt peptide P50416
alteration type single base exchange
alteration region CDS
DNA changes c.197C>T
cDNA.299C>T
g.51070C>T
AA changes T66I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 66
frameshift no
known variant Reference ID: rs80356776
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs65657 (pathogenic for Carnitine palmitoyltransferase 1A deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042690)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042690)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042690)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-4.3070
5.9291
(flanking)4.8961
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 increased51077wt: 0.9556 / mu: 0.9572 (marginal change - not scored)wt: CGGATGTTTAATACTTCCCGGATCCCAGGAGAGGAGACAGG
mu: CGGATGTTTAATATTTCCCGGATCCCAGGAGAGGAGACAGG		 ccgg|ATCC
Acc increased51075wt: 0.55 / mu: 0.72wt: AGCGGATGTTTAATACTTCCCGGATCCCAGGAGAGGAGACA
mu: AGCGGATGTTTAATATTTCCCGGATCCCAGGAGAGGAGACA		 tccc|GGAT
Acc increased51076wt: 0.47 / mu: 0.63wt: GCGGATGTTTAATACTTCCCGGATCCCAGGAGAGGAGACAG
mu: GCGGATGTTTAATATTTCCCGGATCCCAGGAGAGGAGACAG		 cccg|GATC
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      66LCSAQWERMFNTSRIPGEETDDLP
mutated  not conserved    66ERMFNISRIPGEETDDL
Ptroglodytes  all identical  ENSPTRG00000003987  314ERMFNTSRIPGEETDTI
Mmulatta  all identical  ENSMMUG00000001780  314ERMFNTSRIPGEETDTI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000024900  314ERLFNTSRIPGEETDTI
Ggallus  all identical  ENSGALG00000007077  314ERMFNTSRIPGEESDTL
Trubripes  all identical  ENSTRUG00000009681  315ERMFNTTRVPGVETDTL
Drerio  all identical  ENSDARG00000062054  314ERMFNTSRVPGVETDVL
Dmelanogaster  all identical  FBgn0261862  313RTFNTARVPGLETD
Celegans  all identical  Y46G5A.17  316YERLFNTCRVPGEEVDRL
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
4873TRANSMEMHelical; (Potential).lost
74102TOPO_DOMMitochondrial intermembrane (Potential).might get lost (downstream of altered splice site)
103122TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
123773TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
473473ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
479479CONFLICTP -> Q (in Ref. 1; AAC41748).might get lost (downstream of altered splice site)
555567REGIONCoenzyme A binding (By similarity).might get lost (downstream of altered splice site)
568568CONFLICTA -> T (in Ref. 1; AAC41748).might get lost (downstream of altered splice site)
588588MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
589589BINDINGCarnitine (By similarity).might get lost (downstream of altered splice site)
602602BINDINGCarnitine (By similarity).might get lost (downstream of altered splice site)
604604MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
741741MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
747747MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 237 / 237
position (AA) of stopcodon in wt / mu AA sequence 79 / 79
position of stopcodon in wt / mu cDNA 339 / 339
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 103 / 103
chromosome 11
strand -1
last intron/exon boundary 326
theoretical NMD boundary in CDS 173
length of CDS 237
coding sequence (CDS) position 197
cDNA position
(for ins/del: last normal base / first normal base)		 299
gDNA position
(for ins/del: last normal base / first normal base)		 51070
chromosomal position
(for ins/del: last normal base / first normal base)		 68560809
original gDNA sequence snippet GTGGGAGCGGATGTTTAATACTTCCCGGATCCCAGGAGAGG
altered gDNA sequence snippet GTGGGAGCGGATGTTTAATATTTCCCGGATCCCAGGAGAGG
original cDNA sequence snippet GTGGGAGCGGATGTTTAATACTTCCCGGATCCCAGGAGAGG
altered cDNA sequence snippet GTGGGAGCGGATGTTTAATATTTCCCGGATCCCAGGAGAGG
wildtype AA sequence MVNSNYYAMD LLYILPTHIQ AARAGNAIHA ILLYRRKLDR EEIKPIRLLG STIPLCSAQW
ERMFNTSRIP GEETDDLP*
mutated AA sequence MVNSNYYAMD LLYILPTHIQ AARAGNAIHA ILLYRRKLDR EEIKPIRLLG STIPLCSAQW
ERMFNISRIP GEETDDLP*
speed 0.93 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