Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999998186 (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) | chr19:43420451G>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | PSG6 |
| Ensembl transcript ID | ENST00000402603 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q00889 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.253C>G
cDNA.343C>G
g.1712C>G |
| AA changes | H85D Score: 81 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 85 |
| frameshift | no |
| known variant | Reference ID: rs3198831
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 565 | 1141 | 1706 |
| ExAC | 8673 | 15421 | 24094 |
|
| regulatory features | N/A |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.071 | 0 | | -1.114 | 0 | | (flanking) | 1.424 | 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 | 1705 | wt: 0.8905 / mu: 0.9188 (marginal change - not scored) | wt: TACCATTACATTACATCATATGTAGTACACGGTCAAATTAT
mu: TACCATTACATTACATCATATGTAGTAGACGGTCAAATTAT | atat|GTAG | | Donor increased | 1709 | wt: 0.23 / mu: 0.27 | wt: ATGTAGTACACGGTC
mu: ATGTAGTAGACGGTC | GTAG|taca | | Donor increased | 1716 | wt: 0.48 / mu: 0.65 | wt: ACACGGTCAAATTAT
mu: AGACGGTCAAATTAT | ACGG|tcaa |
|
| distance from splice site | 175 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 85 | D | L | Y | H | Y | I | T | S | Y | V | V | H | G | Q | I | I | Y | G | P | A | Y | S | G | R |
| mutated | not conserved | | 85 | D | L | Y | H | Y | I | T | S | Y | V | V | D | G | Q | I | I | Y | G | P | A | Y | S | G |
| Ptroglodytes | no homologue | | | |
| Mmulatta | no homologue | | | |
| 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 | | | 35 | 143 | DOMAIN | Ig-like V-type. | lost | | 103 | 103 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 110 | 110 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 126 | 128 | MOTIF | Cell attachment site (Potential). | might get lost (downstream of altered splice site) | | 148 | 148 | CONFLICT | P -> R (in Ref. 3; CAA34957). | might get lost (downstream of altered splice site) | | 148 | 233 | DOMAIN | Ig-like C2-type 1. | might get lost (downstream of altered splice site) | | 168 | 168 | DISULFID | Probable. | might get lost (downstream of altered splice site) | | 198 | 198 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 216 | 216 | DISULFID | Probable. | might get lost (downstream of altered splice site) | | 220 | 221 | CONFLICT | NP -> RG (in Ref. 3; CAA34957). | might get lost (downstream of altered splice site) | | 241 | 326 | DOMAIN | Ig-like C2-type 2. | might get lost (downstream of altered splice site) | | 261 | 261 | DISULFID | Probable. | might get lost (downstream of altered splice site) | | 267 | 267 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 302 | 302 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 309 | 309 | DISULFID | Probable. | might get lost (downstream of altered splice site) | | 334 | 405 | DOMAIN | Ig-like C2-type 3. | might get lost (downstream of altered splice site) | | 339 | 339 | CONFLICT | S -> Y (in Ref. 3; CAA34957). | might get lost (downstream of altered splice site) | | 353 | 353 | DISULFID | Probable. | might get lost (downstream of altered splice site) | | 364 | 364 | CONFLICT | S -> F (in Ref. 2; AAA36512 and 3; CAA34957). | might get lost (downstream of altered splice site) | | 386 | 386 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 393 | 393 | DISULFID | Probable. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 996 / 996 |
| position (AA) of stopcodon in wt / mu AA sequence | 332 / 332 |
| position of stopcodon in wt / mu cDNA | 1086 / 1086 |
| 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 | 91 / 91 |
| chromosome | 19 |
| strand | -1 |
| last intron/exon boundary | 1052 |
| theoretical NMD boundary in CDS | 911 |
| length of CDS | 996 |
| coding sequence (CDS) position | 253 |
cDNA position
(for ins/del: last normal base / first normal base) | 343 |
gDNA position
(for ins/del: last normal base / first normal base) | 1712 |
chromosomal position
(for ins/del: last normal base / first normal base) | 43420451 |
| original gDNA sequence snippet | ACATTACATCATATGTAGTACACGGTCAAATTATATATGGG |
| altered gDNA sequence snippet | ACATTACATCATATGTAGTAGACGGTCAAATTATATATGGG |
| original cDNA sequence snippet | ACATTACATCATATGTAGTACACGGTCAAATTATATATGGG |
| altered cDNA sequence snippet | ACATTACATCATATGTAGTAGACGGTCAAATTATATATGGG |
| wildtype AA sequence | MGPLSAPPCT QHITWKGLLL TASLLNFWNL PTTAQVIIEA KPPKVSEGKD VLLLVHNLPQ
NLTGYIWYKG QMTDLYHYIT SYVVHGQIIY GPAYSGRETV YSNASLLIQN VTQEDAGSYT
LHIIKRGDGT GGVTGYFTVT LYSETPKPSI SSSNLNPREV MEAVRLICDP ETPDASYLWL
LNGQNLPMTH RLQLSKTNRT LYLFGVTKYI AGPYECEIRN PVSASRSDPV TLNLLHGPDL
PRIYPSFTYY RSGENLDLSC FADSNPPAEY SWTINGKFQL SGQKLFIPQI TTNHSGLYAC
SVRNSATGKE ISKSMIVKVS GPCHGNQTES H* |
| mutated AA sequence | MGPLSAPPCT QHITWKGLLL TASLLNFWNL PTTAQVIIEA KPPKVSEGKD VLLLVHNLPQ
NLTGYIWYKG QMTDLYHYIT SYVVDGQIIY GPAYSGRETV YSNASLLIQN VTQEDAGSYT
LHIIKRGDGT GGVTGYFTVT LYSETPKPSI SSSNLNPREV MEAVRLICDP ETPDASYLWL
LNGQNLPMTH RLQLSKTNRT LYLFGVTKYI AGPYECEIRN PVSASRSDPV TLNLLHGPDL
PRIYPSFTYY RSGENLDLSC FADSNPPAEY SWTINGKFQL SGQKLFIPQI TTNHSGLYAC
SVRNSATGKE ISKSMIVKVS GPCHGNQTES H* |
| speed | 0.16 s |
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