Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM032558)
  • known disease mutation: rs7523 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:14005522C>AN/A show variant in all transcripts   IGV
HGNC symbol COX10
Ensembl transcript ID ENST00000537334
Genbank transcript ID N/A
UniProt peptide Q12887
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.267C>A
g.32710C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104894555
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs7523 (pathogenic for Mitochondrial complex 4 deficiency, nuclear type 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032558)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032558)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032558)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4031
5.3191
(flanking)-1.2550.66
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -24) | splice site change before start ATG (at aa -22) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased32700wt: 0.9609 / mu: 0.9737 (marginal change - not scored)wt: GGCCCTGTTTCCTGCTTACTTCTGTTGGGACAGGCCTTGCA
mu: GGCCCTGTTTCCTGCTTACTTCTGTTGGGAAAGGCCTTGCA		 actt|CTGT
Acc increased32701wt: 0.55 / mu: 0.61wt: GCCCTGTTTCCTGCTTACTTCTGTTGGGACAGGCCTTGCAT
mu: GCCCTGTTTCCTGCTTACTTCTGTTGGGAAAGGCCTTGCAT		 cttc|TGTT
Donor marginally increased32707wt: 0.6992 / mu: 0.7410 (marginal change - not scored)wt: TGTTGGGACAGGCCT
mu: TGTTGGGAAAGGCCT		 TTGG|gaca
Donor gained327060.99mu: CTGTTGGGAAAGGCC GTTG|ggaa
distance from splice site 38
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
11TRANSITMitochondrion (Potential). - EXACT POSITION UNKNOWNmight get lost (downstream of altered splice site)
174194TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
235255TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
257277TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
280300TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
303303CONFLICTA -> T (in Ref. 1; AAA21148).might get lost (downstream of altered splice site)
309329TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
364384TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
394394CONFLICTY -> H (in Ref. 1; AAA21148).might get lost (downstream of altered splice site)
411431TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 332 / 332
chromosome 17
strand 1
last intron/exon boundary 609
theoretical NMD boundary in CDS 227
length of CDS 681
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 267
gDNA position
(for ins/del: last normal base / first normal base)		 32710
chromosomal position
(for ins/del: last normal base / first normal base)		 14005522
original gDNA sequence snippet CCTGCTTACTTCTGTTGGGACAGGCCTTGCATCCTGTGCTG
altered gDNA sequence snippet CCTGCTTACTTCTGTTGGGAAAGGCCTTGCATCCTGTGCTG
original cDNA sequence snippet CCTGCTTACTTCTGTTGGGACAGGCCTTGCATCCTGTGCTG
altered cDNA sequence snippet CCTGCTTACTTCTGTTGGGAAAGGCCTTGCATCCTGTGCTG
wildtype AA sequence MNRTKNRPLV RGQISPLLAV SFATCCAVPG VAILTLGVNP LTGALGLFNI FLYTCCYTPL
KRISIANTWV GAVVGAIPPV MGWTAATGSL DAGAFLLGGI LYSWQFPHFN ALSWGLREDY
SRGGYCMMSV THPGLCRRVA LRHCLALLVL SAAAPVLDIT TWTFPIMALP INAYISYLGF
RFYVDADRRS SRRLFFCSLW HLPLLLLLML TCKRPSGGGD AGPPPS*
mutated AA sequence N/A
speed 0.74 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