Prediction |
disease causing |
Model: simple_aae, prob: 0.987967094538819 (classification due to ClinVar,
real probability is shown anyway)
(explain) |
Summary |
- amino acid sequence changed
- known disease mutation at this position (HGMD CM993912)
- known disease mutation: rs17880 (pathogenic)
- protein features (might be) affected
- splice site changes
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hyperlink |
analysed issue |
analysis result |
name of alteration | no title |
alteration (phys. location) | chr19:45411100C>TN/A
show variant in all transcripts IGV
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HGNC symbol | APOE |
Ensembl transcript ID | ENST00000252486 |
Genbank transcript ID | NM_000041 |
UniProt peptide | P02649 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.127C>T cDNA.238C>T g.2090C>T |
AA changes | R43C Score: 180 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 43 |
frameshift | no |
known variant | Reference ID: rs121918399
database | homozygous (T/T) | heterozygous | allele carriers |
1000G | - | - | - |
ExAC | 0 | 1 | 1 |
known disease mutation: rs17880 (pathogenic for Lipoprotein glomerulopathy) dbSNP
NCBI variation viewer known disease mutation at this position, please check HGMD for details (HGMD ID CM993912)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993912) known disease mutation at this position, please check HGMD for details (HGMD ID CM993912)
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regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | 0.276 | 0.973 | | 1.117 | 0.995 | (flanking) | 2.094 | 1 | 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 | Donor marginally increased | 2093 | wt: 0.3575 / mu: 0.4335 (marginal change - not scored) | wt: AGCGCTGGGAACTGG mu: AGTGCTGGGAACTGG | CGCT|ggga | Donor increased | 2083 | wt: 0.64 / mu: 0.97 | wt: CAGAGCGGCCAGCGC mu: CAGAGCGGCCAGTGC | GAGC|ggcc |
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distance from splice site | 84 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 43 | L | R | Q | Q | T | E | W | Q | S | G | Q | R | W | E | L | A | L | G | R | F | W | D | Y | L |
mutated | not conserved | | 43 | L | R | Q | Q | T | E | W | Q | S | G | Q | C | W | E | L | A | L | G | R | F | W | D | Y |
Ptroglodytes | all identical | ENSPTRG00000011127 | 43 | L | H | H | L | A | E | W | Q | S | G | Q | R | W | E | L | A | L | G | H | F | W | D | Y |
Mmulatta | no homologue | | | |
Fcatus | no homologue | | | |
Mmusculus | not conserved | ENSMUSG00000002985 | 43 | V | T | D | Q | L | E | W | Q | S | N | Q | P | W | E | Q | A | L | N | R | F | W | D | Y |
Ggallus | no homologue | | | |
Trubripes | not conserved | ENSTRUG00000000934 | 57 | - | - | - | - | - | - | - | - | - | - | - | H | W | Q | G | V | V | N | R | F | W | Q | Y |
Drerio | all identical | ENSDARG00000040295 | 43 | - | - | - | - | - | - | - | - | - | - | - | R | W | E | E | M | V | D | R | F | W | Q | Y |
Dmelanogaster | no homologue | | | |
Celegans | no homologue | | | |
Xtropicalis | all conserved | ENSXETG00000019317 | 46 | - | - | - | - | - | - | - | - | - | - | - | K | W | E | T | A | L | D | S | F | W | L | T |
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protein features | start (aa) | end (aa) | feature | details | | 40 | 42 | TURN | | might get lost (downstream of altered splice site) | 43 | 60 | HELIX | | lost | 63 | 70 | HELIX | | might get lost (downstream of altered splice site) | 73 | 96 | HELIX | | might get lost (downstream of altered splice site) | 80 | 101 | REPEAT | 1. | might get lost (downstream of altered splice site) | 80 | 255 | REGION | 8 X 22 AA approximate tandem repeats. | might get lost (downstream of altered splice site) | 93 | 93 | CARBOHYD | N-linked (Glc) (glycation). | might get lost (downstream of altered splice site) | 97 | 99 | TURN | | might get lost (downstream of altered splice site) | 102 | 123 | REPEAT | 2. | might get lost (downstream of altered splice site) | 106 | 141 | HELIX | | might get lost (downstream of altered splice site) | 124 | 145 | REPEAT | 3. | might get lost (downstream of altered splice site) | 143 | 145 | TURN | | might get lost (downstream of altered splice site) | 146 | 167 | REPEAT | 4. | might get lost (downstream of altered splice site) | 147 | 147 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | 149 | 179 | HELIX | | might get lost (downstream of altered splice site) | 158 | 168 | REGION | LDL receptor binding (Potential). | might get lost (downstream of altered splice site) | 162 | 165 | REGION | Heparin-binding. | might get lost (downstream of altered splice site) | 168 | 189 | REPEAT | 5. | might get lost (downstream of altered splice site) | 180 | 182 | TURN | | might get lost (downstream of altered splice site) | 187 | 190 | TURN | | might get lost (downstream of altered splice site) | 190 | 211 | REPEAT | 6. | might get lost (downstream of altered splice site) | 193 | 198 | HELIX | | might get lost (downstream of altered splice site) | 200 | 202 | STRAND | | might get lost (downstream of altered splice site) | 209 | 217 | HELIX | | might get lost (downstream of altered splice site) | 212 | 212 | CARBOHYD | O-linked (GalNAc...). | might get lost (downstream of altered splice site) | 212 | 233 | REPEAT | 7. | might get lost (downstream of altered splice site) | 228 | 241 | HELIX | | might get lost (downstream of altered splice site) | 229 | 236 | REGION | Heparin-binding. | might get lost (downstream of altered splice site) | 234 | 255 | REPEAT | 8. | might get lost (downstream of altered splice site) | 257 | 283 | HELIX | | might get lost (downstream of altered splice site) | 286 | 303 | HELIX | | might get lost (downstream of altered splice site) | 307 | 307 | CARBOHYD | O-linked (GalNAc...). | might get lost (downstream of altered splice site) | 307 | 309 | STRAND | | might get lost (downstream of altered splice site) | 308 | 308 | CARBOHYD | O-linked (GalNAc...). | might get lost (downstream of altered splice site) |
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length of protein | normal |
AA sequence altered | yes |
position of stopcodon in wt / mu CDS | 954 / 954 |
position (AA) of stopcodon in wt / mu AA sequence | 318 / 318 |
position of stopcodon in wt / mu cDNA | 1065 / 1065 |
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 | 112 / 112 |
chromosome | 19 |
strand | 1 |
last intron/exon boundary | 348 |
theoretical NMD boundary in CDS | 186 |
length of CDS | 954 |
coding sequence (CDS) position | 127 |
cDNA position (for ins/del: last normal base / first normal base) | 238 |
gDNA position (for ins/del: last normal base / first normal base) | 2090 |
chromosomal position (for ins/del: last normal base / first normal base) | 45411100 |
original gDNA sequence snippet | CCGAGTGGCAGAGCGGCCAGCGCTGGGAACTGGCACTGGGT |
altered gDNA sequence snippet | CCGAGTGGCAGAGCGGCCAGTGCTGGGAACTGGCACTGGGT |
original cDNA sequence snippet | CCGAGTGGCAGAGCGGCCAGCGCTGGGAACTGGCACTGGGT |
altered cDNA sequence snippet | CCGAGTGGCAGAGCGGCCAGTGCTGGGAACTGGCACTGGGT |
wildtype AA sequence | MKVLWAALLV TFLAGCQAKV EQAVETEPEP ELRQQTEWQS GQRWELALGR FWDYLRWVQT LSEQVQEELL SSQVTQELRA LMDETMKELK AYKSELEEQL TPVAEETRAR LSKELQAAQA RLGADMEDVC GRLVQYRGEV QAMLGQSTEE LRVRLASHLR KLRKRLLRDA DDLQKRLAVY QAGAREGAER GLSAIRERLG PLVEQGRVRA ATVGSLAGQP LQERAQAWGE RLRARMEEMG SRTRDRLDEV KEQVAEVRAK LEEQAQQIRL QAEAFQARLK SWFEPLVEDM QRQWAGLVEK VQAAVGTSAA PVPSDNH* |
mutated AA sequence | MKVLWAALLV TFLAGCQAKV EQAVETEPEP ELRQQTEWQS GQCWELALGR FWDYLRWVQT LSEQVQEELL SSQVTQELRA LMDETMKELK AYKSELEEQL TPVAEETRAR LSKELQAAQA RLGADMEDVC GRLVQYRGEV QAMLGQSTEE LRVRLASHLR KLRKRLLRDA DDLQKRLAVY QAGAREGAER GLSAIRERLG PLVEQGRVRA ATVGSLAGQP LQERAQAWGE RLRARMEEMG SRTRDRLDEV KEQVAEVRAK LEEQAQQIRL QAEAFQARLK SWFEPLVEDM QRQWAGLVEK VQAAVGTSAA PVPSDNH* |
speed | 0.63 s |
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