Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999999995 (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
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr6:29555864C>TN/A
show variant in all transcripts IGV
|
| HGNC symbol | OR2H2 |
| Ensembl transcript ID | ENST00000383640 |
| Genbank transcript ID | NM_007160 |
| UniProt peptide | O95918 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.143C>T
cDNA.182C>T
g.182C>T |
| AA changes | A48V Score: 64 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 48 |
| frameshift | no |
| known variant | Reference ID: rs1233387
| database | homozygous (T/T) | heterozygous | allele carriers |
| 1000G | 321 | 1076 | 1397 |
| ExAC | 5796 | 21175 | 26971 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.967 | 0 | | 0.014 | 0 | | (flanking) | -0.186 | 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 | | Acc increased | 187 | wt: 0.42 / mu: 0.61 | wt: TCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACTCTCCA
mu: TCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACTCTCCA | ctgg|ACCC | | Acc increased | 180 | wt: 0.67 / mu: 0.84 | wt: ACACTCATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCA
mu: ACACTCATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCA | gtct|GCGC | | Acc increased | 184 | wt: 0.33 / mu: 0.37 | wt: TCATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACTCT
mu: TCATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACTCT | gcgc|TGGA | | Acc marginally increased | 186 | wt: 0.7125 / mu: 0.7516 (marginal change - not scored) | wt: ATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACTCTCC
mu: ATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACTCTCC | gctg|GACC |
|
| distance from splice site | 182 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 48 | L | V | G | N | T | L | I | I | L | L | S | A | L | D | P | K | L | H | S | P | M | Y | F | F |
| mutated | not conserved | | 48 | L | V | G | N | T | L | I | I | L | L | S | V | L | D | P | K | L | H | S | P | M | Y | F |
| Ptroglodytes | not conserved | ENSPTRG00000017900 | 48 | L | V | G | N | T | L | I | I | L | L | S | V | L | D | P | K | L | H | S | P | M | Y | F |
| Mmulatta | not conserved | ENSMMUG00000021482 | 48 | L | V | A | N | T | L | I | I | L | L | S | V | L | D | P | R | L | H | S | P | M | Y | F |
| Fcatus | no homologue | | | |
| Mmusculus | no homologue | | | |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | no homologue | | | |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 24 | 47 | TRANSMEM | Helical; Name=1; (Potential). | might get lost (downstream of altered splice site) | | 48 | 55 | TOPO_DOM | Cytoplasmic (Potential). | lost | | 51 | 51 | CONFLICT | P -> T (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) | | 56 | 77 | TRANSMEM | Helical; Name=2; (Potential). | might get lost (downstream of altered splice site) | | 78 | 98 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 81 | 81 | CONFLICT | V -> A (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) | | 95 | 95 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 99 | 118 | TRANSMEM | Helical; Name=3; (Potential). | might get lost (downstream of altered splice site) | | 113 | 114 | CONFLICT | LT -> MK (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) | | 119 | 137 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 138 | 156 | TRANSMEM | Helical; Name=4; (Potential). | might get lost (downstream of altered splice site) | | 153 | 153 | CONFLICT | E -> G (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) | | 157 | 193 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 187 | 187 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 194 | 217 | TRANSMEM | Helical; Name=5; (Potential). | might get lost (downstream of altered splice site) | | 218 | 234 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 230 | 232 | CONFLICT | KGR -> TAW (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) | | 235 | 257 | TRANSMEM | Helical; Name=6; (Potential). | might get lost (downstream of altered splice site) | | 258 | 270 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 267 | 267 | CONFLICT | E -> G (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) | | 271 | 290 | TRANSMEM | Helical; Name=7; (Potential). | might get lost (downstream of altered splice site) | | 287 | 287 | CONFLICT | I -> V (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) | | 291 | 312 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 295 | 296 | CONFLICT | VT -> IK (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) | | 299 | 299 | CONFLICT | F -> L (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) | | 307 | 312 | CONFLICT | MGLTQS -> RDSRESWRAA (in Ref. 1; AAB36567). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 939 / 939 |
| position (AA) of stopcodon in wt / mu AA sequence | 313 / 313 |
| position of stopcodon in wt / mu cDNA | 978 / 978 |
| 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 | 40 / 40 |
| chromosome | 6 |
| 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 | 939 |
| coding sequence (CDS) position | 143 |
cDNA position
(for ins/del: last normal base / first normal base) | 182 |
gDNA position
(for ins/del: last normal base / first normal base) | 182 |
chromosomal position
(for ins/del: last normal base / first normal base) | 29555864 |
| original gDNA sequence snippet | ACTCATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACT |
| altered gDNA sequence snippet | ACTCATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACT |
| original cDNA sequence snippet | ACTCATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACT |
| altered cDNA sequence snippet | ACTCATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACT |
| wildtype AA sequence | MVNQSSTPGF LLLGFSEHPG LERTLFVVVL TSYLLTLVGN TLIILLSALD PKLHSPMYFF
LSNLSFLDLC FTTSCVPQML VNLWGPKKTI SFLDCSVQIF IFLSLGTTEC ILLTVMAFDR
YVAVCQPLHY ATIIHPRLCW QLASVAWVIG LVESVVQTPS TLHLPFCPDR QVDDFVCEVP
ALIRLSCEDT SYNEIQVAVA SVFILVVPLS LILVSYGAIT WAVLRINSAK GRRKAFGTCS
SHLTVVTLFY SSVIAVYLQP KNPYAQERGK FFGLFYAVGT PSLNPLIYTL RNKEVTRAFR
RLLGKEMGLT QS* |
| mutated AA sequence | MVNQSSTPGF LLLGFSEHPG LERTLFVVVL TSYLLTLVGN TLIILLSVLD PKLHSPMYFF
LSNLSFLDLC FTTSCVPQML VNLWGPKKTI SFLDCSVQIF IFLSLGTTEC ILLTVMAFDR
YVAVCQPLHY ATIIHPRLCW QLASVAWVIG LVESVVQTPS TLHLPFCPDR QVDDFVCEVP
ALIRLSCEDT SYNEIQVAVA SVFILVVPLS LILVSYGAIT WAVLRINSAK GRRKAFGTCS
SHLTVVTLFY SSVIAVYLQP KNPYAQERGK FFGLFYAVGT PSLNPLIYTL RNKEVTRAFR
RLLGKEMGLT QS* |
| speed | 0.11 s |
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