Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997691003 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM890002)
  • known disease mutation: rs1961 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:43249744G>TN/A show variant in all transcripts   IGV
HGNC symbol ADA
Ensembl transcript ID ENST00000537820
Genbank transcript ID N/A
UniProt peptide P00813
alteration type single base exchange
alteration region CDS
DNA changes c.818C>A
cDNA.902C>A
g.31131C>A
AA changes P273Q Score: 76 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 273
frameshift no
known variant Reference ID: rs121908718
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1961 (pathogenic for Severe combined immunodeficiency due to ADA deficiency|Partial adenosine deaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.5810
4.2580.999
(flanking)4.2271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained311260.39mu: ACAGATGACCAGCTC AGAT|gacc
distance from splice site 45
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      273DQANYSLNTDDPLIFKSTLDTDYQ
mutated  not conserved    273DQANYSLNTDDQLIFKSTLDTDY
Ptroglodytes  all identical  ENSPTRG00000013524  297DQANYSLNTDDPLIF
Mmulatta  all identical  ENSMMUG00000010603  297DQANYSLNTDDPLIF
Fcatus  all identical  ENSFCAG00000002474  330DQANYSLNTDDPLIF
Mmusculus  all identical  ENSMUSG00000017697  297DKANYSLNTDDPLIF
Ggallus  all identical  ENSGALG00000004170  295DQANYSINTDDPLIFNSNID
Trubripes  all identical  ENSTRUG00000010199  301DPLIFNSSLHLDY
Drerio  all identical  ENSDARG00000003113  299DKANYSLNTDDPTIFNST
Dmelanogaster  no homologue    
Celegans  all identical  C06G3.5  330DDVNFSVSRDDPTCFD
Xtropicalis  all identical  ENSXETG00000003459  293DKANYSLNTDDPLIFGSTL
protein features
start (aa)end (aa)featuredetails 
270272STRANDmight get lost (downstream of altered splice site)
279285HELIXmight get lost (downstream of altered splice site)
290292STRANDmight get lost (downstream of altered splice site)
295295METALZinc; catalytic.might get lost (downstream of altered splice site)
296296BINDINGSubstrate.might get lost (downstream of altered splice site)
297300HELIXmight get lost (downstream of altered splice site)
304315HELIXmight get lost (downstream of altered splice site)
319331HELIXmight get lost (downstream of altered splice site)
333335STRANDmight get lost (downstream of altered splice site)
337351HELIXmight get lost (downstream of altered splice site)
340340CONFLICTK -> R (in Ref. 5; BAD97117).might get lost (downstream of altered splice site)
355362HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1020 / 1020
position (AA) of stopcodon in wt / mu AA sequence 340 / 340
position of stopcodon in wt / mu cDNA 1104 / 1104
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 85 / 85
chromosome 20
strand -1
last intron/exon boundary 1091
theoretical NMD boundary in CDS 956
length of CDS 1020
coding sequence (CDS) position 818
cDNA position
(for ins/del: last normal base / first normal base)		 902
gDNA position
(for ins/del: last normal base / first normal base)		 31131
chromosomal position
(for ins/del: last normal base / first normal base)		 43249744
original gDNA sequence snippet CTCGCTCAACACAGATGACCCGCTCATCTTCAAGTCCACCC
altered gDNA sequence snippet CTCGCTCAACACAGATGACCAGCTCATCTTCAAGTCCACCC
original cDNA sequence snippet CTCGCTCAACACAGATGACCCGCTCATCTTCAAGTCCACCC
altered cDNA sequence snippet CTCGCTCAACACAGATGACCAGCTCATCTTCAAGTCCACCC
wildtype AA sequence MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQAVDILKTE RLGHGYHTLE DQALYNRLRQ ENMHFEICPW
SSYLTGAWKP DTEHAVIRLK NDQANYSLNT DDPLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINAAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*
mutated AA sequence MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD
FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA
EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI
DLAGDETIPG SSLLPGHVQA YQAVDILKTE RLGHGYHTLE DQALYNRLRQ ENMHFEICPW
SSYLTGAWKP DTEHAVIRLK NDQANYSLNT DDQLIFKSTL DTDYQMTKRD MGFTEEEFKR
LNINAAKSSF LPEDEKRELL DLLYKAYGMP PSASAGQNL*
speed 0.50 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