Prediction |
polymorphism |
Model: simple_aae, prob: 0.0874751314205942 (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) | chr11:5842356A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | OR52N2 |
| Ensembl transcript ID | ENST00000317037 |
| Genbank transcript ID | NM_001005174 |
| UniProt peptide | Q8NGI0 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.791A>G
cDNA.813A>G
g.813A>G |
| AA changes | H264R Score: 29 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 264 |
| frameshift | no |
| known variant | Reference ID: rs8181512
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 546 | 1183 | 1729 |
| ExAC | 16212 | 343 | 16555 |
|
| regulatory features | N/A |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 3.972 | 0.986 | | 4.669 | 0.986 | | (flanking) | -0.764 | 0.321 |
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 | 811 | wt: 0.21 / mu: 0.34 | wt: GCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAA
mu: GCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAA | cact|CATC | | Acc marginally increased | 814 | wt: 0.9030 / mu: 0.9043 (marginal change - not scored) | wt: TTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAATAT
mu: TTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAATAT | tcat|CGTT | | Acc marginally increased | 809 | wt: 0.9894 / mu: 0.9934 (marginal change - not scored) | wt: CTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACAC
mu: CTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACAC | ttca|CTCA | | Acc marginally increased | 806 | wt: 0.9604 / mu: 0.9773 (marginal change - not scored) | wt: TTGCTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGA
mu: TTGCTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGA | tttt|TCAC | | Acc increased | 821 | wt: 0.34 / mu: 0.44 | wt: CTTTTTTCACTCATCGTTTTGTAGGACACAATATCCCAAAC
mu: CTTTTTTCACTCGTCGTTTTGTAGGACACAATATCCCAAAC | tttg|TAGG | | Acc marginally increased | 807 | wt: 0.9830 / mu: 0.9841 (marginal change - not scored) | wt: TGCTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGAC
mu: TGCTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGAC | tttt|CACT | | Acc marginally increased | 824 | wt: 0.8844 / mu: 0.8905 (marginal change - not scored) | wt: TTTTCACTCATCGTTTTGTAGGACACAATATCCCAAACCAC
mu: TTTTCACTCGTCGTTTTGTAGGACACAATATCCCAAACCAC | gtag|GACA | | Acc marginally increased | 803 | wt: 0.9874 / mu: 0.9883 (marginal change - not scored) | wt: ATGTTGCTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTA
mu: ATGTTGCTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTA | actt|TTTT | | Acc marginally increased | 822 | wt: 0.8641 / mu: 0.8913 (marginal change - not scored) | wt: TTTTTTCACTCATCGTTTTGTAGGACACAATATCCCAAACC
mu: TTTTTTCACTCGTCGTTTTGTAGGACACAATATCCCAAACC | ttgt|AGGA | | Acc marginally increased | 810 | wt: 0.9836 / mu: 0.9854 (marginal change - not scored) | wt: TGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACA
mu: TGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACA | tcac|TCAT | | Acc increased | 820 | wt: 0.74 / mu: 0.90 | wt: ACTTTTTTCACTCATCGTTTTGTAGGACACAATATCCCAAA
mu: ACTTTTTTCACTCGTCGTTTTGTAGGACACAATATCCCAAA | tttt|GTAG | | Acc marginally increased | 805 | wt: 0.7587 / mu: 0.8037 (marginal change - not scored) | wt: GTTGCTGCTTTTTTCACTTTTTTCACTCATCGTTTTGTAGG
mu: GTTGCTGCTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGG | tttt|TTCA | | Acc marginally increased | 812 | wt: 0.9963 / mu: 0.9979 (marginal change - not scored) | wt: CTTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAAT
mu: CTTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAAT | actc|ATCG |
|
| distance from splice site | 223 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 264 | T | Y | V | A | A | F | F | T | F | F | T | H | R | F | V | G | H | N | I | P | N | H | I | H |
| mutated | not conserved | | 264 | T | Y | V | A | A | F | F | T | F | F | T | R | R | F | V | G | H | N | I | P | N | H | I |
| Ptroglodytes | all identical | ENSPTRG00000003265 | 264 | T | Y | V | P | A | F | F | T | F | F | T | H | R | F | G | G | H | N | I | P | N | H | I |
| Mmulatta | no homologue | | | |
| Fcatus | all identical | ENSFCAG00000007096 | 264 | T | Y | V | P | A | L | F | T | I | F | T | H | R | F | G | G | Q | N | I | P | H | H | V |
| 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 | | | 261 | 276 | TOPO_DOM | Extracellular (Potential). | lost | | 277 | 297 | TRANSMEM | Helical; Name=7; (Potential). | might get lost (downstream of altered splice site) | | 298 | 321 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 966 / 966 |
| position (AA) of stopcodon in wt / mu AA sequence | 322 / 322 |
| position of stopcodon in wt / mu cDNA | 988 / 988 |
| 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 | 23 / 23 |
| chromosome | 11 |
| 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 | 966 |
| coding sequence (CDS) position | 791 |
cDNA position
(for ins/del: last normal base / first normal base) | 813 |
gDNA position
(for ins/del: last normal base / first normal base) | 813 |
chromosomal position
(for ins/del: last normal base / first normal base) | 5842356 |
| original gDNA sequence snippet | TTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAATA |
| altered gDNA sequence snippet | TTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAATA |
| original cDNA sequence snippet | TTTTTTCACTTTTTTCACTCATCGTTTTGTAGGACACAATA |
| altered cDNA sequence snippet | TTTTTTCACTTTTTTCACTCGTCGTTTTGTAGGACACAATA |
| wildtype AA sequence | MSGDNSSSLT PGFFILNGVP GLEATHIWIS LPFCFMYIIA VVGNCGLICL ISHEEALHRP
MYYFLALLSF TDVTLCTTMV PNMLCIFWFN LKEIDFNACL AQMFFVHMLT GMESGVLMLM
ALDRYVAICY PLRYATILTN PVIAKAGLAT FLRNVMLIIP FTLLTKRLPY CRGNFIPHTY
CDHMSVAKVS CGNFKVNAIY GLMVALLIGV FDICCISVSY TMILQAVMSL SSADARHKAF
STCTSHMCSI VITYVAAFFT FFTHRFVGHN IPNHIHIIVA NLYLLLPPTM NPIVYGVKTK
QIQEGVIKFL LGDKVSFTYD K* |
| mutated AA sequence | MSGDNSSSLT PGFFILNGVP GLEATHIWIS LPFCFMYIIA VVGNCGLICL ISHEEALHRP
MYYFLALLSF TDVTLCTTMV PNMLCIFWFN LKEIDFNACL AQMFFVHMLT GMESGVLMLM
ALDRYVAICY PLRYATILTN PVIAKAGLAT FLRNVMLIIP FTLLTKRLPY CRGNFIPHTY
CDHMSVAKVS CGNFKVNAIY GLMVALLIGV FDICCISVSY TMILQAVMSL SSADARHKAF
STCTSHMCSI VITYVAAFFT FFTRRFVGHN IPNHIHIIVA NLYLLLPPTM NPIVYGVKTK
QIQEGVIKFL LGDKVSFTYD K* |
| speed | 1.32 s |
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