Prediction |
polymorphism |
Model: simple_aae, prob: 0.0726827879290891 (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 CM994452)
- protein features (might be) affected
- splice site changes
|
hyperlink |
analysed issue |
analysis result |
name of alteration | no title |
alteration (phys. location) | chr4:41259633C>AN/A
show variant in all transcripts IGV
|
HGNC symbol | UCHL1 |
Ensembl transcript ID | ENST00000512788 |
Genbank transcript ID | N/A |
UniProt peptide | P09936 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.53C>A cDNA.85C>A g.1204C>A |
AA changes | S18Y Score: 144 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 18 |
frameshift | no |
known variant | Reference ID: rs5030732
database | homozygous (A/A) | heterozygous | allele carriers |
1000G | 263 | 746 | 1009 |
ExAC | 1168 | 6233 | 7401 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM994452)
|
regulatory features | DNase1, Open Chromatin, DNase1 Hypersensitive Site H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation H3K9ac, Histone, Histone 3 Lysine 9 Acetylation PolII, Polymerase, RNA Polymerase II Promoter Associated, Regulatory Feature, Promoter like regulatory feature TAF1, Transcription Factor, TAF1 Transcription Factor Binding |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | -0.042 | 0.951 | | 0.634 | 0.953 | (flanking) | 1.319 | 0.955 | 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 decreased | 1196 | wt: 0.9949 / mu: 0.9941 (marginal change - not scored) | wt: CGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGT mu: CGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGT | gcag|GTGC | Acc marginally increased | 1194 | wt: 0.9748 / mu: 0.9793 (marginal change - not scored) | wt: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGG mu: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGG | ccgc|AGGT | Acc increased | 1207 | wt: 0.35 / mu: 0.46 | wt: CTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCCAGT mu: CTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCCAGT | cccg|GCTG |
|
distance from splice site | 8 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 18 | E | I | N | P | E | M | L | N | K | V | L | S | R | L | G | V | A | G | Q | W | R | F | V | D |
mutated | not conserved | | 18 | E | I | N | P | E | M | L | N | K | V | L | Y | R | L | G | V | A | G | Q | W | R | F | V |
Ptroglodytes | all identical | ENSPTRG00000016009 | 18 | E | I | N | P | E | V | S | A | R | V | L | S | R | L | G | V | A | G | Q | W | R | F | V |
Mmulatta | all identical | ENSMMUG00000013071 | 18 | E | I | N | P | E | M | L | N | K | V | L | S | R | L | G | V | A | G | Q | W | R | F | V |
Fcatus | no homologue | | | |
Mmusculus | all conserved | ENSMUSG00000029223 | 18 | E | I | N | P | E | M | L | N | K | V | L | A | K | L | G | V | A | G | Q | W | R | F | A |
Ggallus | all identical | ENSGALG00000014261 | 19 | E | I | N | P | E | M | L | N | K | V | L | S | R | L | G | V | S | P | G | W | R | F | V |
Trubripes | no homologue | | | |
Drerio | all identical | ENSDARG00000026871 | 18 | E | I | N | P | E | M | L | N | K | V | L | S | K | L | G | V | G | S | K | W | R | F | V |
Dmelanogaster | not conserved | FBgn0010288 | 19 | E | S | N | P | E | V | L | T | K | Y | I | H | K | L | G | V | S | P | A | W | S | V | T |
Celegans | not conserved | F46E10.8 | 20 | E | S | N | P | S | V | I | N | P | M | I | E | K | M | G | V | S | G | V | - | K | T | V |
Xtropicalis | all conserved | ENSXETG00000021089 | 29 | | | | | | | L | S | E | V | L | A | Q | L | G | V | L | D | G | W | K | F | V |
|
protein features | start (aa) | end (aa) | feature | details | | 10 | 19 | HELIX | | lost | 24 | 31 | STRAND | | might get lost (downstream of altered splice site) | 36 | 40 | HELIX | | might get lost (downstream of altered splice site) | 46 | 54 | STRAND | | might get lost (downstream of altered splice site) | 57 | 70 | HELIX | | might get lost (downstream of altered splice site) | 71 | 74 | TURN | | might get lost (downstream of altered splice site) | 73 | 73 | MUTAGEN | Q->R: No effect on enzymatic parameters. | might get lost (downstream of altered splice site) | 86 | 88 | STRAND | | might get lost (downstream of altered splice site) | 90 | 90 | MUTAGEN | C->S: Abolishes enzymatic activity. | might get lost (downstream of altered splice site) | 90 | 90 | ACT_SITE | Nucleophile. | might get lost (downstream of altered splice site) | 90 | 100 | HELIX | | might get lost (downstream of altered splice site) | 97 | 97 | MUTAGEN | H->Q,N: 2-fold increase in affinity for ubiquitin ethyl ester, slight reduction in enzymatic activity. | might get lost (downstream of altered splice site) | 101 | 105 | TURN | | might get lost (downstream of altered splice site) | 113 | 120 | HELIX | | might get lost (downstream of altered splice site) | 121 | 123 | TURN | | might get lost (downstream of altered splice site) | 124 | 124 | SITE | Susceptible to oxidation. | might get lost (downstream of altered splice site) | 126 | 134 | HELIX | | might get lost (downstream of altered splice site) | 137 | 147 | HELIX | | might get lost (downstream of altered splice site) | 160 | 168 | STRAND | | might get lost (downstream of altered splice site) | 161 | 161 | MUTAGEN | H->D: 10000-fold decrease in enzymatic activity; no change in affinity for ubiquitin ethyl ester. | might get lost (downstream of altered splice site) | 161 | 161 | MUTAGEN | H->K,Q,N,Y: Abolishes enzymatic activity. | might get lost (downstream of altered splice site) | 161 | 161 | ACT_SITE | Proton donor. | might get lost (downstream of altered splice site) | 171 | 175 | STRAND | | might get lost (downstream of altered splice site) | 176 | 176 | SITE | Important for enzyme activity. | might get lost (downstream of altered splice site) | 176 | 176 | MUTAGEN | D->N: 6-fold decrease in affinity for ubiquitin ethyl ester; 97.5% decrease in enzymatic activity. | might get lost (downstream of altered splice site) | 179 | 179 | SITE | Susceptible to oxidation. | might get lost (downstream of altered splice site) | 179 | 181 | STRAND | | might get lost (downstream of altered splice site) | 183 | 187 | STRAND | | might get lost (downstream of altered splice site) | 190 | 192 | HELIX | | might get lost (downstream of altered splice site) | 193 | 207 | HELIX | | might get lost (downstream of altered splice site) | 204 | 204 | MUTAGEN | F->A: Almost complete loss of activity. | might get lost (downstream of altered splice site) | 211 | 213 | HELIX | | might get lost (downstream of altered splice site) | 211 | 216 | REGION | Interaction with ubiquitin. | might get lost (downstream of altered splice site) | 215 | 221 | STRAND | | might get lost (downstream of altered splice site) | 220 | 220 | SITE | Susceptible to oxidation. | might get lost (downstream of altered splice site) | 220 | 220 | LIPID | S-farnesyl cysteine. | might get lost (downstream of altered splice site) | 221 | 223 | PROPEP | Removed in mature form (Probable). /FTId=PRO_0000414311. | might get lost (downstream of altered splice site) |
|
length of protein | normal |
AA sequence altered | yes |
position of stopcodon in wt / mu CDS | 726 / 726 |
position (AA) of stopcodon in wt / mu AA sequence | 242 / 242 |
position of stopcodon in wt / mu cDNA | 758 / 758 |
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 | 33 / 33 |
chromosome | 4 |
strand | 1 |
last intron/exon boundary | 647 |
theoretical NMD boundary in CDS | 564 |
length of CDS | 726 |
coding sequence (CDS) position | 53 |
cDNA position (for ins/del: last normal base / first normal base) | 85 |
gDNA position (for ins/del: last normal base / first normal base) | 1204 |
chromosomal position (for ins/del: last normal base / first normal base) | 41259633 |
original gDNA sequence snippet | CTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCC |
altered gDNA sequence snippet | CTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCC |
original cDNA sequence snippet | GATGCTGAACAAAGTGCTGTCCCGGCTGGGGGTCGCCGGCC |
altered cDNA sequence snippet | GATGCTGAACAAAGTGCTGTACCGGCTGGGGGTCGCCGGCC |
wildtype AA sequence | MQLKPMEINP EMLNKVLSRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE TEKMSPEDRA KCFEKNEAIQ AAHDAVAQEG QCRVDDKVNF HFILFNNVDG HLYELDGRMP FPVNHGASSE DTLLKVIFGM HLFLMTLPRS AENSPSVSKE KSASLPWLSA RQPNALWEGL C* |
mutated AA sequence | MQLKPMEINP EMLNKVLYRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE TEKMSPEDRA KCFEKNEAIQ AAHDAVAQEG QCRVDDKVNF HFILFNNVDG HLYELDGRMP FPVNHGASSE DTLLKVIFGM HLFLMTLPRS AENSPSVSKE KSASLPWLSA RQPNALWEGL C* |
speed | 0.90 s |
|
|