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: ENST00000221992
Querying Taster for transcript #2: ENST00000405816
MT speed 1.36 s - this script 3.394137 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CEACAM5polymorphism_automatic4.7795101210113e-13simple_aaeI80Vsingle base exchangers12971352show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999522 (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
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:42213772A>GN/A show variant in all transcripts   IGV
HGNC symbol CEACAM5
Ensembl transcript ID ENST00000221992
Genbank transcript ID NM_004363
UniProt peptide P06731
alteration type single base exchange
alteration region CDS
DNA changes c.238A>G
cDNA.385A>G
g.1269A>G
AA changes I80V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 80
frameshift no
known variant Reference ID: rs12971352
databasehomozygous (G/G)heterozygousallele carriers
1000G132554686
ExAC19131377715690
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4540.013
-0.1120.002
(flanking)-2.7210
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 174
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      80KGERVDGNRQIIGYVIGTQQATPG
mutated  all conserved    80KGERVDGNRQIVGYVIGTQQATP
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
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 
35144DOMAINIg-like 1.lost
7883STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2109 / 2109
position (AA) of stopcodon in wt / mu AA sequence 703 / 703
position of stopcodon in wt / mu cDNA 2256 / 2256
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 148 / 148
chromosome 19
strand 1
last intron/exon boundary 2293
theoretical NMD boundary in CDS 2095
length of CDS 2109
coding sequence (CDS) position 238
cDNA position
(for ins/del: last normal base / first normal base)		 385
gDNA position
(for ins/del: last normal base / first normal base)		 1269
chromosomal position
(for ins/del: last normal base / first normal base)		 42213772
original gDNA sequence snippet TGGATGGCAACCGTCAAATTATAGGATATGTAATAGGAACT
altered gDNA sequence snippet TGGATGGCAACCGTCAAATTGTAGGATATGTAATAGGAACT
original cDNA sequence snippet TGGATGGCAACCGTCAAATTATAGGATATGTAATAGGAACT
altered cDNA sequence snippet TGGATGGCAACCGTCAAATTGTAGGATATGTAATAGGAACT
wildtype AA sequence MESPSAPPHR WCIPWQRLLL TASLLTFWNP PTTAKLTIES TPFNVAEGKE VLLLVHNLPQ
HLFGYSWYKG ERVDGNRQII GYVIGTQQAT PGPAYSGREI IYPNASLLIQ NIIQNDTGFY
TLHVIKSDLV NEEATGQFRV YPELPKPSIS SNNSKPVEDK DAVAFTCEPE TQDATYLWWV
NNQSLPVSPR LQLSNGNRTL TLFNVTRNDT ASYKCETQNP VSARRSDSVI LNVLYGPDAP
TISPLNTSYR SGENLNLSCH AASNPPAQYS WFVNGTFQQS TQELFIPNIT VNNSGSYTCQ
AHNSDTGLNR TTVTTITVYA EPPKPFITSN NSNPVEDEDA VALTCEPEIQ NTTYLWWVNN
QSLPVSPRLQ LSNDNRTLTL LSVTRNDVGP YECGIQNKLS VDHSDPVILN VLYGPDDPTI
SPSYTYYRPG VNLSLSCHAA SNPPAQYSWL IDGNIQQHTQ ELFISNITEK NSGLYTCQAN
NSASGHSRTT VKTITVSAEL PKPSISSNNS KPVEDKDAVA FTCEPEAQNT TYLWWVNGQS
LPVSPRLQLS NGNRTLTLFN VTRNDARAYV CGIQNSVSAN RSDPVTLDVL YGPDTPIISP
PDSSYLSGAN LNLSCHSASN PSPQYSWRIN GIPQQHTQVL FIAKITPNNN GTYACFVSNL
ATGRNNSIVK SITVSASGTS PGLSAGATVG IMIGVLVGVA LI*
mutated AA sequence MESPSAPPHR WCIPWQRLLL TASLLTFWNP PTTAKLTIES TPFNVAEGKE VLLLVHNLPQ
HLFGYSWYKG ERVDGNRQIV GYVIGTQQAT PGPAYSGREI IYPNASLLIQ NIIQNDTGFY
TLHVIKSDLV NEEATGQFRV YPELPKPSIS SNNSKPVEDK DAVAFTCEPE TQDATYLWWV
NNQSLPVSPR LQLSNGNRTL TLFNVTRNDT ASYKCETQNP VSARRSDSVI LNVLYGPDAP
TISPLNTSYR SGENLNLSCH AASNPPAQYS WFVNGTFQQS TQELFIPNIT VNNSGSYTCQ
AHNSDTGLNR TTVTTITVYA EPPKPFITSN NSNPVEDEDA VALTCEPEIQ NTTYLWWVNN
QSLPVSPRLQ LSNDNRTLTL LSVTRNDVGP YECGIQNKLS VDHSDPVILN VLYGPDDPTI
SPSYTYYRPG VNLSLSCHAA SNPPAQYSWL IDGNIQQHTQ ELFISNITEK NSGLYTCQAN
NSASGHSRTT VKTITVSAEL PKPSISSNNS KPVEDKDAVA FTCEPEAQNT TYLWWVNGQS
LPVSPRLQLS NGNRTLTLFN VTRNDARAYV CGIQNSVSAN RSDPVTLDVL YGPDTPIISP
PDSSYLSGAN LNLSCHSASN PSPQYSWRIN GIPQQHTQVL FIAKITPNNN GTYACFVSNL
ATGRNNSIVK SITVSASGTS PGLSAGATVG IMIGVLVGVA LI*
speed 1.36 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