Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999999883789785 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:501900C>AN/A show variant in all transcripts   IGV
HGNC symbol MADCAM1
Ensembl transcript ID ENST00000346144
Genbank transcript ID NM_130762
UniProt peptide Q13477
alteration type single base exchange
alteration region intron
DNA changes g.12725C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs3745925
databasehomozygous (A/A)heterozygousallele carriers
1000G140808948
ExAC77371627935
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6320.001
-0.2430
(flanking)-2.0680
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased12728wt: 0.21 / mu: 0.30wt: GCCCACGCAGGGAGA
mu: GCACACGCAGGGAGA		 CCAC|gcag
Donor marginally increased12727wt: 0.2743 / mu: 0.3304 (marginal change - not scored)wt: GGCCCACGCAGGGAG
mu: GGCACACGCAGGGAG		 CCCA|cgca
Donor increased12717wt: 0.49 / mu: 0.63wt: TCCCAGGCTGGGCCC
mu: TCCCAGGCTGGGCAC		 CCAG|gctg
distance from splice site 2845
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
19317TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
113231DOMAINIg-like 2.might get lost (downstream of altered splice site)
213223STRANDmight get lost (downstream of altered splice site)
226317REGIONMucin-like.might get lost (downstream of altered splice site)
228231REPEAT1; truncated.might get lost (downstream of altered splice site)
228271REGION5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.might get lost (downstream of altered splice site)
232239REPEAT2.might get lost (downstream of altered splice site)
240240CONFLICTS -> P (in Ref. 2; AAB02194 and 3; AAC51354).might get lost (downstream of altered splice site)
240247REPEAT3.might get lost (downstream of altered splice site)
242242CONFLICTD -> N (in Ref. 2; AAB02194 and 3; AAC51354).might get lost (downstream of altered splice site)
248255REPEAT4.might get lost (downstream of altered splice site)
254254CONFLICTQ -> P (in Ref. 1; AAC13661).might get lost (downstream of altered splice site)
256263REPEAT5.might get lost (downstream of altered splice site)
264271REPEAT6.might get lost (downstream of altered splice site)
318338TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
339382TOPO_DOMCytoplasmic (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 47 / 47
chromosome 19
strand 1
last intron/exon boundary 714
theoretical NMD boundary in CDS 617
length of CDS 888
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 12725
chromosomal position
(for ins/del: last normal base / first normal base)		 501900
original gDNA sequence snippet TGAGATCTCCCAGGCTGGGCCCACGCAGGGAGAAGTGATCC
altered gDNA sequence snippet TGAGATCTCCCAGGCTGGGCACACGCAGGGAGAAGTGATCC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDFGLALLLA GLLGLLLGQS LQVKPLQVEP PEPVVAVALG ASRQLTCRLA CADRGASVQW
RGLDTSLGAV QSDTGRSVLT VRNASLSAAG TRVCVGSCGG RTFQHTVQLL VYAFPDQLTV
SPAALVPGDP EVACTAHKVT PVDPNALSFS LLVGGQELEG AQALGPEVQE EEEEPQGDED
VLFRVTERWR LPPLGTPVPP ALYCQATMRL PGLELSHRQA IPASKPAGDQ LPAALWTSSA
VLGLLLLALP TYHLWKRCRH LAEDDTHPPA SLRLLPQVSA WAGLRGTGQV GISPS*
mutated AA sequence N/A
speed 0.54 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