Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999965986 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
Summary |
- amino acid sequence changed
- homozygous in TGP or ExAC
- protein features (might be) affected
- splice site changes
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hyperlink |
analysed issue |
analysis result |
name of alteration | no title |
alteration (phys. location) | chr9:107361642G>AN/A
show variant in all transcripts IGV
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HGNC symbol | OR13C5 |
Ensembl transcript ID | ENST00000374779 |
Genbank transcript ID | NM_001004482 |
UniProt peptide | Q8NGS8 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.53C>T cDNA.147C>T g.147C>T |
AA changes | S18F Score: 155 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 18 |
frameshift | no |
known variant | Reference ID: rs1851722
database | homozygous (A/A) | heterozygous | allele carriers |
1000G | 190 | 825 | 1015 |
ExAC | 3884 | 20775 | 24659 |
|
regulatory features | N/A |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | 0.081 | 0 | | 1.141 | 0.002 | (flanking) | -0.391 | 0.001 | 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 | Acc marginally increased | 137 | wt: 0.6140 / mu: 0.6644 (marginal change - not scored) | wt: TTCTGGTGGAATTTTTTCTGAAGGGACTTTCTGGTCACCCA mu: TTCTGGTGGAATTTTTTCTGAAGGGACTTTTTGGTCACCCA | ctga|AGGG | Acc increased | 158 | wt: 0.34 / mu: 0.47 | wt: AGGGACTTTCTGGTCACCCAAGACTTGAGTTACTCTTTTTT mu: AGGGACTTTTTGGTCACCCAAGACTTGAGTTACTCTTTTTT | ccaa|GACT | Acc increased | 149 | wt: 0.24 / mu: 0.27 | wt: TTTTTCTGAAGGGACTTTCTGGTCACCCAAGACTTGAGTTA mu: TTTTTCTGAAGGGACTTTTTGGTCACCCAAGACTTGAGTTA | tctg|GTCA | Donor marginally increased | 138 | wt: 0.9252 / mu: 0.9296 (marginal change - not scored) | wt: TCTGAAGGGACTTTC mu: TCTGAAGGGACTTTT | TGAA|ggga | Acc gained | 156 | 0.31 | mu: GAAGGGACTTTTTGGTCACCCAAGACTTGAGTTACTCTTTT | accc|AAGA |
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distance from splice site | 147 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 18 | T | I | L | V | E | F | F | L | K | G | L | S | G | H | P | R | L | E | L | L | F | F | V | L |
mutated | not conserved | | 18 | T | I | L | V | E | F | F | L | K | G | L | F | G | H | P | R | L | E | L | L | F | F | V |
Ptroglodytes | all identical | ENSPTRG00000029179 | 18 | T | I | L | V | E | F | F | L | K | G | L | S | G | H | P | R | L | E | L | L | F | F | V |
Mmulatta | all identical | ENSMMUG00000009754 | 18 | T | I | L | V | E | F | F | L | K | G | L | S | G | Y | P | R | L | E | L | L | F | F | V |
Fcatus | no homologue | | | |
Mmusculus | no homologue | | | |
Ggallus | no homologue | | | |
Trubripes | no homologue | | | |
Drerio | no homologue | | | |
Dmelanogaster | no homologue | | | |
Celegans | no homologue | | | |
Xtropicalis | no homologue | | | |
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protein features | start (aa) | end (aa) | feature | details | | 1 | 25 | TOPO_DOM | Extracellular (Potential). | lost | 26 | 46 | TRANSMEM | Helical; Name=1; (Potential). | might get lost (downstream of altered splice site) | 47 | 54 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | 55 | 75 | TRANSMEM | Helical; Name=2; (Potential). | might get lost (downstream of altered splice site) | 76 | 99 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | 97 | 97 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | 100 | 120 | TRANSMEM | Helical; Name=3; (Potential). | might get lost (downstream of altered splice site) | 121 | 139 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | 140 | 160 | TRANSMEM | Helical; Name=4; (Potential). | might get lost (downstream of altered splice site) | 161 | 197 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | 189 | 189 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | 198 | 217 | TRANSMEM | Helical; Name=5; (Potential). | might get lost (downstream of altered splice site) | 218 | 237 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | 238 | 258 | TRANSMEM | Helical; Name=6; (Potential). | might get lost (downstream of altered splice site) | 259 | 277 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | 278 | 298 | TRANSMEM | Helical; Name=7; (Potential). | might get lost (downstream of altered splice site) | 299 | 318 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) |
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length of protein | normal |
AA sequence altered | yes |
position of stopcodon in wt / mu CDS | 957 / 957 |
position (AA) of stopcodon in wt / mu AA sequence | 319 / 319 |
position of stopcodon in wt / mu cDNA | 1051 / 1051 |
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 | 95 / 95 |
chromosome | 9 |
strand | -1 |
last intron/exon boundary | 1 |
theoretical NMD boundary in CDS | cannot be calculated, too little distance between start ATG and last intron/exon boundary |
length of CDS | 957 |
coding sequence (CDS) position | 53 |
cDNA position (for ins/del: last normal base / first normal base) | 147 |
gDNA position (for ins/del: last normal base / first normal base) | 147 |
chromosomal position (for ins/del: last normal base / first normal base) | 107361642 |
original gDNA sequence snippet | ATTTTTTCTGAAGGGACTTTCTGGTCACCCAAGACTTGAGT |
altered gDNA sequence snippet | ATTTTTTCTGAAGGGACTTTTTGGTCACCCAAGACTTGAGT |
original cDNA sequence snippet | ATTTTTTCTGAAGGGACTTTCTGGTCACCCAAGACTTGAGT |
altered cDNA sequence snippet | ATTTTTTCTGAAGGGACTTTTTGGTCACCCAAGACTTGAGT |
wildtype AA sequence | MEWENHTILV EFFLKGLSGH PRLELLFFVL IFIMYVVILL GNGTLILISI LDPHLHTPMY FFLGNLSFLD ICYTTTSIPS TLVSFLSERK TISLSGCAVQ MFLSLAMGTT ECVLLGVMAF DRYVAICNPL RYPIIMSKDA YVPMAAGSWI IGAVNSAVQT VFVVQLPFCR NNIINHFTCE ILAVMKLACA DISGNEFILL VTTTLFLLTP LLLIIVSYTL IILSIFKISS SEGRSKPSST CSARLTVVIT FCGTIFLMYM KPKSQETLNS DDLDATDKLI FIFYRVMTPM MNPLIYSLRN KDVKEAVKHL LRRKNFNK* |
mutated AA sequence | MEWENHTILV EFFLKGLFGH PRLELLFFVL IFIMYVVILL GNGTLILISI LDPHLHTPMY FFLGNLSFLD ICYTTTSIPS TLVSFLSERK TISLSGCAVQ MFLSLAMGTT ECVLLGVMAF DRYVAICNPL RYPIIMSKDA YVPMAAGSWI IGAVNSAVQT VFVVQLPFCR NNIINHFTCE ILAVMKLACA DISGNEFILL VTTTLFLLTP LLLIIVSYTL IILSIFKISS SEGRSKPSST CSARLTVVIT FCGTIFLMYM KPKSQETLNS DDLDATDKLI FIFYRVMTPM MNPLIYSLRN KDVKEAVKHL LRRKNFNK* |
speed | 1.03 s |
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