Prediction |
polymorphism |
Model: without_aae, prob: 0.999971515663534 (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) | chr1:248202344G>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | OR2L13 |
| Ensembl transcript ID | ENST00000366478 |
| Genbank transcript ID | NM_175911 |
| UniProt peptide | Q8N349 |
| alteration type | single base exchange |
| alteration region | intron |
| DNA changes | g.101852G>C |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs6658141
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 480 | 768 | 1248 |
| ExAC | 4000 | 15947 | 19947 |
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.936 | 0 | | 1.217 | 0.006 | | (flanking) | 1.03 | 0.006 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | splice site change before start ATG (at aa -47) | | effect | gDNA position | score | detection sequence | exon-intron border | | Acc marginally increased | 101849 | wt: 0.9087 / mu: 0.9474 (marginal change - not scored) | wt: ATGCACCCTTTGCTTATACCTATGTACGTCCAAGATCCCTG
mu: ATGCACCCTTTGCTTATACCTATCTACGTCCAAGATCCCTG | acct|ATGT | | Acc increased | 101861 | wt: 0.68 / mu: 0.81 | wt: CTTATACCTATGTACGTCCAAGATCCCTGCGATCTCCAACA
mu: CTTATACCTATCTACGTCCAAGATCCCTGCGATCTCCAACA | ccaa|GATC | | Acc marginally increased | 101850 | wt: 0.4998 / mu: 0.5123 (marginal change - not scored) | wt: TGCACCCTTTGCTTATACCTATGTACGTCCAAGATCCCTGC
mu: TGCACCCTTTGCTTATACCTATCTACGTCCAAGATCCCTGC | ccta|TGTA | | Acc marginally increased | 101853 | wt: 0.6027 / mu: 0.6437 (marginal change - not scored) | wt: ACCCTTTGCTTATACCTATGTACGTCCAAGATCCCTGCGAT
mu: ACCCTTTGCTTATACCTATCTACGTCCAAGATCCCTGCGAT | atgt|ACGT | | Acc marginally increased | 101855 | wt: 0.9115 / mu: 0.9474 (marginal change - not scored) | wt: CCTTTGCTTATACCTATGTACGTCCAAGATCCCTGCGATCT
mu: CCTTTGCTTATACCTATCTACGTCCAAGATCCCTGCGATCT | gtac|GTCC | | Acc marginally increased | 101843 | wt: 0.8954 / mu: 0.9255 (marginal change - not scored) | wt: TCTACTATGCACCCTTTGCTTATACCTATGTACGTCCAAGA
mu: TCTACTATGCACCCTTTGCTTATACCTATCTACGTCCAAGA | gctt|ATAC | | Donor marginally increased | 101850 | wt: 0.9138 / mu: 0.9465 (marginal change - not scored) | wt: TACCTATGTACGTCC
mu: TACCTATCTACGTCC | CCTA|tgta | | Donor marginally increased | 101856 | wt: 0.9623 / mu: 0.9860 (marginal change - not scored) | wt: TGTACGTCCAAGATC
mu: TCTACGTCCAAGATC | TACG|tcca | | Acc gained | 101854 | 0.50 | mu: CCCTTTGCTTATACCTATCTACGTCCAAGATCCCTGCGATC | tcta|CGTC |
|
| distance from splice site | 59609 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 24 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 5 | 5 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 20 | 20 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 25 | 48 | TRANSMEM | Helical; Name=1; (Potential). | might get lost (downstream of altered splice site) | | 49 | 56 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 57 | 78 | TRANSMEM | Helical; Name=2; (Potential). | might get lost (downstream of altered splice site) | | 79 | 99 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 96 | 96 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 100 | 119 | TRANSMEM | Helical; Name=3; (Potential). | might get lost (downstream of altered splice site) | | 120 | 138 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 139 | 157 | TRANSMEM | Helical; Name=4; (Potential). | might get lost (downstream of altered splice site) | | 158 | 194 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 188 | 188 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 195 | 218 | TRANSMEM | Helical; Name=5; (Potential). | might get lost (downstream of altered splice site) | | 219 | 235 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 236 | 258 | TRANSMEM | Helical; Name=6; (Potential). | might get lost (downstream of altered splice site) | | 259 | 271 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 272 | 291 | TRANSMEM | Helical; Name=7; (Potential). | might get lost (downstream of altered splice site) | | 292 | 312 | 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 | 338 / 338 |
| chromosome | 1 |
| strand | 1 |
| last intron/exon boundary | 320 |
| theoretical NMD boundary in CDS | cannot be calculated, too little distance between start ATG and last intron/exon boundary |
| length of CDS | 939 |
| 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) | 101852 |
chromosomal position
(for ins/del: last normal base / first normal base) | 248202344 |
| original gDNA sequence snippet | CACCCTTTGCTTATACCTATGTACGTCCAAGATCCCTGCGA |
| altered gDNA sequence snippet | CACCCTTTGCTTATACCTATCTACGTCCAAGATCCCTGCGA |
| original cDNA sequence snippet | N/A |
| altered cDNA sequence snippet | N/A |
| wildtype AA sequence | MEKWNHTSND FILLGLLPPN QTGIFLLCLI ILIFFLASVG NSAMIHLIHV DPRLHTPMYF
LLSQLSLMDL MYISTTVPKM AYNFLSGQKG ISFLGCGVQS FFFLTMACSE GLLLTSMAYD
RYLAICHSLY YPIRMSKMMC VKMIGGSWTL GSINSLAHTV FALHIPYCRS RAIDHFFCDV
PAMLLLACTD TWVYEYMVFV STSLFLLFPF IGITSSCGRV LFAVYHMHSK EGRKKAFTTI
STHLTVVIFY YAPFVYTYLR PRNLRSPAED KILAVFYTIL TPMLNPIIYS LRNKEVLGAM
RRVFGIFSFL KE* |
| mutated AA sequence | N/A |
| speed | 0.81 s |
|
|
