Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99772893954373 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012083)
  • known disease mutation: rs12742 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:87017523C>TN/A show variant in all transcripts   IGV
HGNC symbol CD8A
Ensembl transcript ID ENST00000538832
Genbank transcript ID N/A
UniProt peptide P01732
alteration type single base exchange
alteration region CDS
DNA changes c.454G>A
cDNA.772G>A
g.17997G>A
AA changes G152S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 152
frameshift no
known variant Reference ID: rs121918660
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs12742 (pathogenic for Cd8 deficiency, familial) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012083)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012083)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012083)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7630.999
2.7630.968
(flanking)-0.9340.053
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained179930.75mu: GAGAACGAGAGCTAC GAAC|gaga
Donor gained179920.74mu: AGAGAACGAGAGCTA AGAA|cgag
Donor gained179970.83mu: ACGAGAGCTACTATT GAGA|gcta
distance from splice site 73
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      152LTLSDFRRENEGYYFCSALSNSIM
mutated  not conserved    152LTLSDFRRENESYYFCSALSNSI
Ptroglodytes  all identical  ENSPTRG00000012159  152LTLSDFRRENEGYYFCSALSNSI
Mmulatta  all identical  ENSMMUG00000003524  111LTLRDFRQENEGYYFCSALSN
Fcatus  all identical  ENSFCAG00000014826  114LTLHRFRKEEEGYYFCS
Mmusculus  all identical  ENSMUSG00000053977  120LTLNKFSKENEGYY
Ggallus  all identical  ENSGALG00000015816  115LVVKNFRAQDQGTYFCI
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
22182TOPO_DOMExtracellular (Potential).lost
183203TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
204235TOPO_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 831 / 831
position (AA) of stopcodon in wt / mu AA sequence 277 / 277
position of stopcodon in wt / mu cDNA 1149 / 1149
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 319 / 319
chromosome 2
strand -1
last intron/exon boundary 1098
theoretical NMD boundary in CDS 729
length of CDS 831
coding sequence (CDS) position 454
cDNA position
(for ins/del: last normal base / first normal base)		 772
gDNA position
(for ins/del: last normal base / first normal base)		 17997
chromosomal position
(for ins/del: last normal base / first normal base)		 87017523
original gDNA sequence snippet ACTTCCGCCGAGAGAACGAGGGCTACTATTTCTGCTCGGCC
altered gDNA sequence snippet ACTTCCGCCGAGAGAACGAGAGCTACTATTTCTGCTCGGCC
original cDNA sequence snippet ACTTCCGCCGAGAGAACGAGGGCTACTATTTCTGCTCGGCC
altered cDNA sequence snippet ACTTCCGCCGAGAGAACGAGAGCTACTATTTCTGCTCGGCC
wildtype AA sequence MRNQAPGRPK GATFPPRRPT GSRAPPLAPE LRAKQRPGER VMALPVTALL LPLALLLHAA
RPSQFRVSPL DRTWNLGETV ELKCQVLLSN PTSGCSWLFQ PRGAAASPTF LLYLSQNKPK
AAEGLDTQRF SGKRLGDTFV LTLSDFRREN EGYYFCSALS NSIMYFSHFV PVFLPAKPTT
TPAPRPPTPA PTIASQPLSL RPEACRPAAG GAVHTRGLDF ACDIYIWAPL AGTCGVLLLS
LVITLYCNHR NRRRVCKCPR PVVKSGDKPS LSARYV*
mutated AA sequence MRNQAPGRPK GATFPPRRPT GSRAPPLAPE LRAKQRPGER VMALPVTALL LPLALLLHAA
RPSQFRVSPL DRTWNLGETV ELKCQVLLSN PTSGCSWLFQ PRGAAASPTF LLYLSQNKPK
AAEGLDTQRF SGKRLGDTFV LTLSDFRREN ESYYFCSALS NSIMYFSHFV PVFLPAKPTT
TPAPRPPTPA PTIASQPLSL RPEACRPAAG GAVHTRGLDF ACDIYIWAPL AGTCGVLLLS
LVITLYCNHR NRRRVCKCPR PVVKSGDKPS LSARYV*
speed 0.72 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