Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999999996 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- amino acid sequence changed
- homozygous in TGP or ExAC
- known disease mutation at this position (HGMD CM105494)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr17:3480447T>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | TRPV1 |
| Ensembl transcript ID | ENST00000399756 |
| Genbank transcript ID | NM_080706 |
| UniProt peptide | Q8NER1 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.1753A>G
cDNA.2280A>G
g.19946A>G |
| AA changes | I585V Score: 29 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 585 |
| frameshift | no |
| known variant | Reference ID: rs8065080
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 360 | 871 | 1231 |
| ExAC | 5311 | 17262 | 22573 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM105494)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 1.062 | 0.003 | | -0.127 | 0.002 | | (flanking) | 0.012 | 0.031 |
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 | 19947 | wt: 0.6254 / mu: 0.6277 (marginal change - not scored) | wt: CCGTTTCATGTTTGTCTACATCGTCTTCTTGTTCGGGTTTT
mu: CCGTTTCATGTTTGTCTACGTCGTCTTCTTGTTCGGGTTTT | acat|CGTC | | Acc marginally increased | 19956 | wt: 0.9796 / mu: 0.9823 (marginal change - not scored) | wt: GTTTGTCTACATCGTCTTCTTGTTCGGGTTTTCCACAGGTA
mu: GTTTGTCTACGTCGTCTTCTTGTTCGGGTTTTCCACAGGTA | tctt|GTTC | | Acc marginally increased | 19945 | wt: 0.9175 / mu: 0.9642 (marginal change - not scored) | wt: TGCCGTTTCATGTTTGTCTACATCGTCTTCTTGTTCGGGTT
mu: TGCCGTTTCATGTTTGTCTACGTCGTCTTCTTGTTCGGGTT | ctac|ATCG | | Acc increased | 19939 | wt: 0.41 / mu: 0.52 | wt: GACCTGTGCCGTTTCATGTTTGTCTACATCGTCTTCTTGTT
mu: GACCTGTGCCGTTTCATGTTTGTCTACGTCGTCTTCTTGTT | gttt|GTCT | | Acc marginally increased | 19952 | wt: 0.3835 / mu: 0.3941 (marginal change - not scored) | wt: TCATGTTTGTCTACATCGTCTTCTTGTTCGGGTTTTCCACA
mu: TCATGTTTGTCTACGTCGTCTTCTTGTTCGGGTTTTCCACA | gtct|TCTT | | Acc marginally increased | 19957 | wt: 0.9091 / mu: 0.9162 (marginal change - not scored) | wt: TTTGTCTACATCGTCTTCTTGTTCGGGTTTTCCACAGGTAA
mu: TTTGTCTACGTCGTCTTCTTGTTCGGGTTTTCCACAGGTAA | cttg|TTCG | | Acc increased | 19953 | wt: 0.22 / mu: 0.36 | wt: CATGTTTGTCTACATCGTCTTCTTGTTCGGGTTTTCCACAG
mu: CATGTTTGTCTACGTCGTCTTCTTGTTCGGGTTTTCCACAG | tctt|CTTG | | Acc marginally increased | 19941 | wt: 0.2636 / mu: 0.2878 (marginal change - not scored) | wt: CCTGTGCCGTTTCATGTTTGTCTACATCGTCTTCTTGTTCG
mu: CCTGTGCCGTTTCATGTTTGTCTACGTCGTCTTCTTGTTCG | ttgt|CTAC | | Acc marginally increased | 19950 | wt: 0.2244 / mu: 0.2269 (marginal change - not scored) | wt: TTTCATGTTTGTCTACATCGTCTTCTTGTTCGGGTTTTCCA
mu: TTTCATGTTTGTCTACGTCGTCTTCTTGTTCGGGTTTTCCA | tcgt|CTTC | | Acc increased | 19955 | wt: 0.74 / mu: 0.87 | wt: TGTTTGTCTACATCGTCTTCTTGTTCGGGTTTTCCACAGGT
mu: TGTTTGTCTACGTCGTCTTCTTGTTCGGGTTTTCCACAGGT | ttct|TGTT | | Acc marginally increased | 19937 | wt: 0.6521 / mu: 0.6907 (marginal change - not scored) | wt: GAGACCTGTGCCGTTTCATGTTTGTCTACATCGTCTTCTTG
mu: GAGACCTGTGCCGTTTCATGTTTGTCTACGTCGTCTTCTTG | atgt|TTGT | | Donor gained | 19940 | 0.78 | mu: TGTTTGTCTACGTCG | TTTG|tcta |
|
| distance from splice site | 28 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 585 | L | R | D | L | C | R | F | M | F | V | Y | I | V | F | L | F | G | F | S | T | A | V | V | T |
| mutated | all conserved | | 585 | L | R | D | L | C | R | F | M | F | V | Y | V | V | F | L | F | G | F | S | T | A | V | V |
| Ptroglodytes | all conserved | ENSPTRG00000024045 | 532 | L | R | D | L | C | R | F | M | F | V | Y | V | V | F | L | F | G | F | S | T | A | V | V |
| Mmulatta | all conserved | ENSMMUG00000000711 | 585 | L | R | D | L | C | R | F | M | F | V | Y | V | V | F | L | F | G | F | S | T | - | V | M |
| Fcatus | no homologue | | | |
| Mmusculus | all conserved | ENSMUSG00000005952 | 586 | L | R | D | L | C | R | F | M | F | V | Y | L | V | F | L | F | G | F | S | T | A | V | V |
| Ggallus | all conserved | ENSGALG00000004649 | 593 | L | R | D | L | C | R | F | M | F | V | Y | L | V | F | L | L | G | F | S | T | A | V | V |
| Trubripes | no homologue | | | |
| Drerio | all conserved | ENSDARG00000059883 | 553 | L | G | E | I | R | R | F | L | V | V | Y | M | V | F | L | I | G | F | S | A | A | L | V |
| Dmelanogaster | all conserved | FBgn0036414 | 627 | M | G | D | L | L | R | F | V | S | I | Y | L | V | F | V | M | G | F | S | Q | A | F | Y |
| Celegans | not conserved | B0212.5 | 545 | | | | | | | | | | | | A | I | F | L | V | S | F | S | Q | V | F | Y |
| Xtropicalis | all conserved | ENSXETG00000005790 | 594 | | S | D | M | V | R | F | M | F | V | Y | L | L | F | L | F | G | F | A | A | A | L | V |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 580 | 600 | TRANSMEM | Helical; (Potential). | lost | | 604 | 604 | CARBOHYD | N-linked (GlcNAc...) (By similarity). | might get lost (downstream of altered splice site) | | 611 | 647 | INTRAMEM | Pore-forming; (Probable). | might get lost (downstream of altered splice site) | | 660 | 680 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 681 | 839 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 685 | 713 | REGION | AD (By similarity). | might get lost (downstream of altered splice site) | | 705 | 705 | MOD_RES | Phosphothreonine (By similarity). | might get lost (downstream of altered splice site) | | 768 | 802 | REGION | Interaction with calmodulin (By similarity). | might get lost (downstream of altered splice site) | | 775 | 775 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 778 | 793 | REGION | Required for PIP2-mediated channel inhibition (By similarity). | might get lost (downstream of altered splice site) | | 801 | 801 | MOD_RES | Phosphoserine; by PKC/PRKCE (By similarity). | might get lost (downstream of altered splice site) | | 821 | 821 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 2520 / 2520 |
| position (AA) of stopcodon in wt / mu AA sequence | 840 / 840 |
| position of stopcodon in wt / mu cDNA | 3047 / 3047 |
| 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 | 528 / 528 |
| chromosome | 17 |
| strand | -1 |
| last intron/exon boundary | 2875 |
| theoretical NMD boundary in CDS | 2297 |
| length of CDS | 2520 |
| coding sequence (CDS) position | 1753 |
cDNA position
(for ins/del: last normal base / first normal base) | 2280 |
gDNA position
(for ins/del: last normal base / first normal base) | 19946 |
chromosomal position
(for ins/del: last normal base / first normal base) | 3480447 |
| original gDNA sequence snippet | GCCGTTTCATGTTTGTCTACATCGTCTTCTTGTTCGGGTTT |
| altered gDNA sequence snippet | GCCGTTTCATGTTTGTCTACGTCGTCTTCTTGTTCGGGTTT |
| original cDNA sequence snippet | GCCGTTTCATGTTTGTCTACATCGTCTTCTTGTTCGGGTTT |
| altered cDNA sequence snippet | GCCGTTTCATGTTTGTCTACGTCGTCTTCTTGTTCGGGTTT |
| wildtype AA sequence | MKKWSSTDLG AAADPLQKDT CPDPLDGDPN SRPPPAKPQL STAKSRTRLF GKGDSEEAFP
VDCPHEEGEL DSCPTITVSP VITIQRPGDG PTGARLLSQD SVAASTEKTL RLYDRRSIFE
AVAQNNCQDL ESLLLFLQKS KKHLTDNEFK DPETGKTCLL KAMLNLHDGQ NTTIPLLLEI
ARQTDSLKEL VNASYTDSYY KGQTALHIAI ERRNMALVTL LVENGADVQA AAHGDFFKKT
KGRPGFYFGE LPLSLAACTN QLGIVKFLLQ NSWQTADISA RDSVGNTVLH ALVEVADNTA
DNTKFVTSMY NEILMLGAKL HPTLKLEELT NKKGMTPLAL AAGTGKIGVL AYILQREIQE
PECRHLSRKF TEWAYGPVHS SLYDLSCIDT CEKNSVLEVI AYSSSETPNR HDMLLVEPLN
RLLQDKWDRF VKRIFYFNFL VYCLYMIIFT MAAYYRPVDG LPPFKMEKTG DYFRVTGEIL
SVLGGVYFFF RGIQYFLQRR PSMKTLFVDS YSEMLFFLQS LFMLATVVLY FSHLKEYVAS
MVFSLALGWT NMLYYTRGFQ QMGIYAVMIE KMILRDLCRF MFVYIVFLFG FSTAVVTLIE
DGKNDSLPSE STSHRWRGPA CRPPDSSYNS LYSTCLELFK FTIGMGDLEF TENYDFKAVF
IILLLAYVIL TYILLLNMLI ALMGETVNKI AQESKNIWKL QRAITILDTE KSFLKCMRKA
FRSGKLLQVG YTPDGKDDYR WCFRVDEVNW TTWNTNVGII NEDPGNCEGV KRTLSFSLRS
SRVSGRHWKN FALVPLLREA SARDRQSAQP EEVYLRQFSG SLKPEDAEVF KSPAASGEK* |
| mutated AA sequence | MKKWSSTDLG AAADPLQKDT CPDPLDGDPN SRPPPAKPQL STAKSRTRLF GKGDSEEAFP
VDCPHEEGEL DSCPTITVSP VITIQRPGDG PTGARLLSQD SVAASTEKTL RLYDRRSIFE
AVAQNNCQDL ESLLLFLQKS KKHLTDNEFK DPETGKTCLL KAMLNLHDGQ NTTIPLLLEI
ARQTDSLKEL VNASYTDSYY KGQTALHIAI ERRNMALVTL LVENGADVQA AAHGDFFKKT
KGRPGFYFGE LPLSLAACTN QLGIVKFLLQ NSWQTADISA RDSVGNTVLH ALVEVADNTA
DNTKFVTSMY NEILMLGAKL HPTLKLEELT NKKGMTPLAL AAGTGKIGVL AYILQREIQE
PECRHLSRKF TEWAYGPVHS SLYDLSCIDT CEKNSVLEVI AYSSSETPNR HDMLLVEPLN
RLLQDKWDRF VKRIFYFNFL VYCLYMIIFT MAAYYRPVDG LPPFKMEKTG DYFRVTGEIL
SVLGGVYFFF RGIQYFLQRR PSMKTLFVDS YSEMLFFLQS LFMLATVVLY FSHLKEYVAS
MVFSLALGWT NMLYYTRGFQ QMGIYAVMIE KMILRDLCRF MFVYVVFLFG FSTAVVTLIE
DGKNDSLPSE STSHRWRGPA CRPPDSSYNS LYSTCLELFK FTIGMGDLEF TENYDFKAVF
IILLLAYVIL TYILLLNMLI ALMGETVNKI AQESKNIWKL QRAITILDTE KSFLKCMRKA
FRSGKLLQVG YTPDGKDDYR WCFRVDEVNW TTWNTNVGII NEDPGNCEGV KRTLSFSLRS
SRVSGRHWKN FALVPLLREA SARDRQSAQP EEVYLRQFSG SLKPEDAEVF KSPAASGEK* |
| speed | 1.06 s |
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