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 | ENST00000402456 |
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 |
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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 |
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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 | | | |
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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 | 885 / 885 |
position (AA) of stopcodon in wt / mu AA sequence | 295 / 295 |
position of stopcodon in wt / mu cDNA | 975 / 975 |
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 | 518 |
theoretical NMD boundary in CDS | 377 |
length of CDS | 885 |
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 TLNLLREYLL FLCEPGCHPK YKWPEARPLS PSQVQVQRPL SLNIKAGHDF LLQANQSRPR LDQQ* |
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 TLNLLREYLL FLCEPGCHPK YKWPEARPLS PSQVQVQRPL SLNIKAGHDF LLQANQSRPR LDQQ* |
speed | 0.21 s |
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