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 | ENST00000382683 |
| Genbank transcript ID | N/A |
| 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
| database | homozygous (A/A) | heterozygous | allele carriers |
| 1000G | 140 | 808 | 948 |
| ExAC | 773 | 7162 | 7935 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.632 | 0.001 | | -0.243 | 0 | | (flanking) | -2.068 | 0 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | | effect | gDNA position | score | wt detection sequence | exon-intron border | | Donor increased | 12728 | wt: 0.21 / mu: 0.30 | wt: GCCCACGCAGGGAGA
mu: GCACACGCAGGGAGA | CCAC|gcag | | Donor marginally increased | 12727 | wt: 0.2743 / mu: 0.3304 (marginal change - not scored) | wt: GGCCCACGCAGGGAG
mu: GGCACACGCAGGGAG | CCCA|cgca | | Donor increased | 12717 | wt: 0.49 / mu: 0.63 | wt: 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) | feature | details | | | 19 | 317 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 113 | 231 | DOMAIN | Ig-like 2. | might get lost (downstream of altered splice site) | | 131 | 140 | STRAND | | might get lost (downstream of altered splice site) | | 134 | 134 | DISULFID | | might get lost (downstream of altered splice site) | | 144 | 146 | TURN | | might get lost (downstream of altered splice site) | | 147 | 153 | STRAND | | might get lost (downstream of altered splice site) | | 167 | 170 | STRAND | | might get lost (downstream of altered splice site) | | 175 | 177 | STRAND | | might get lost (downstream of altered splice site) | | 183 | 190 | STRAND | | might get lost (downstream of altered splice site) | | 200 | 210 | STRAND | | might get lost (downstream of altered splice site) | | 204 | 204 | DISULFID | | might get lost (downstream of altered splice site) | | 213 | 223 | STRAND | | might get lost (downstream of altered splice site) | | 226 | 317 | REGION | Mucin-like. | might get lost (downstream of altered splice site) | | 228 | 231 | REPEAT | 1; truncated. | might get lost (downstream of altered splice site) | | 228 | 271 | REGION | 5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E. | might get lost (downstream of altered splice site) | | 232 | 239 | REPEAT | 2. | might get lost (downstream of altered splice site) | | 240 | 240 | CONFLICT | S -> P (in Ref. 2; AAB02194 and 3; AAC51354). | might get lost (downstream of altered splice site) | | 240 | 247 | REPEAT | 3. | might get lost (downstream of altered splice site) | | 242 | 242 | CONFLICT | D -> N (in Ref. 2; AAB02194 and 3; AAC51354). | might get lost (downstream of altered splice site) | | 248 | 255 | REPEAT | 4. | might get lost (downstream of altered splice site) | | 254 | 254 | CONFLICT | Q -> P (in Ref. 1; AAC13661). | might get lost (downstream of altered splice site) | | 256 | 263 | REPEAT | 5. | might get lost (downstream of altered splice site) | | 264 | 271 | REPEAT | 6. | might get lost (downstream of altered splice site) | | 318 | 338 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 339 | 382 | TOPO_DOM | Cytoplasmic (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 | 1 / 1 |
| chromosome | 19 |
| strand | 1 |
| last intron/exon boundary | 383 |
| theoretical NMD boundary in CDS | 332 |
| length of CDS | 603 |
| 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 GLLGLLLAFP DQLTVSPAAL VPGDPEVACT AHKVTPVDPN ALSFSLLVGG
QELEGAQALG PEVQEEEEEP QGDEDVLFRV TERWRLPPLG TPVPPALYCQ ATMRLPGLEL
SHRQAIPASK PAGDQLPAAL WTSSAVLGLL LLALPTYHLW KRCRHLAEDD THPPASLRLL
PQVSAWAGLR GTGQVGISPS * |
| mutated AA sequence | N/A |
| speed | 0.59 s |
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