Prediction |
polymorphism |
Model: simple_aae, prob: 0.99999999999997 (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) | chr19:55174498T>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | LILRB4 |
| Ensembl transcript ID | ENST00000270452 |
| Genbank transcript ID | NM_006847 |
| UniProt peptide | Q8NHJ6 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.13T>C
cDNA.375T>C
g.19159T>C |
| AA changes | F5L Score: 22 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 5 |
| frameshift | no |
| known variant | Reference ID: rs28366008
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 256 | 1013 | 1269 |
| ExAC | 4079 | 22550 | 26629 |
|
| 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 |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -1.484 | 0 | | -0.054 | 0.003 | | (flanking) | 1.627 | 0.018 |
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 | 19163 | wt: 0.8957 / mu: 0.9009 (marginal change - not scored) | wt: CGCCATGATCCCCACCTTCACGGCTCTGCTCTGCCTCGGTG
mu: CGCCATGATCCCCACCCTCACGGCTCTGCTCTGCCTCGGTG | tcac|GGCT | | Donor increased | 19158 | wt: 0.30 / mu: 0.60 | wt: CCCACCTTCACGGCT
mu: CCCACCCTCACGGCT | CACC|ttca |
|
| distance from splice site | 22 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 5 | | | | | | | | M | I | P | T | F | T | A | L | L | C | L | G | L | S | L | G | P |
| mutated | not conserved | | 5 | | | | | | | | M | I | P | T | L | T | A | L | L | C | L | G | L | S | L | G | P | R | T | H | M | Q |
| Ptroglodytes | not conserved | ENSPTRG00000011468 | 5 | | | | | | | | M | I | P | T | L | T | A | L | L | C | L | G | L | S | L | G | P | R | T | H | V | Q |
| Mmulatta | no homologue | | | |
| Fcatus | not conserved | ENSFCAG00000003601 | 5 | | | | | | | | M | T | P | T | L | T | T | L | L | L | L | G | L | S | V | G | P | R | T | R | A | Q |
| 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 | | | 1 | 21 | SIGNAL | Potential. | lost | | 22 | 259 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 27 | 118 | DOMAIN | Ig-like C2-type 1. | might get lost (downstream of altered splice site) | | 30 | 35 | STRAND | | might get lost (downstream of altered splice site) | | 37 | 40 | STRAND | | might get lost (downstream of altered splice site) | | 45 | 50 | STRAND | | might get lost (downstream of altered splice site) | | 49 | 49 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 57 | 62 | STRAND | | might get lost (downstream of altered splice site) | | 69 | 72 | STRAND | | might get lost (downstream of altered splice site) | | 76 | 87 | STRAND | | might get lost (downstream of altered splice site) | | 90 | 92 | HELIX | | might get lost (downstream of altered splice site) | | 94 | 102 | STRAND | | might get lost (downstream of altered splice site) | | 98 | 98 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 105 | 107 | STRAND | | might get lost (downstream of altered splice site) | | 113 | 118 | STRAND | | might get lost (downstream of altered splice site) | | 124 | 218 | DOMAIN | Ig-like C2-type 2. | might get lost (downstream of altered splice site) | | 125 | 130 | STRAND | | might get lost (downstream of altered splice site) | | 132 | 135 | STRAND | | might get lost (downstream of altered splice site) | | 140 | 157 | STRAND | | might get lost (downstream of altered splice site) | | 144 | 144 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 163 | 165 | HELIX | | might get lost (downstream of altered splice site) | | 166 | 182 | STRAND | | might get lost (downstream of altered splice site) | | 187 | 189 | HELIX | | might get lost (downstream of altered splice site) | | 191 | 198 | STRAND | | might get lost (downstream of altered splice site) | | 195 | 195 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 200 | 202 | HELIX | | might get lost (downstream of altered splice site) | | 213 | 218 | STRAND | | might get lost (downstream of altered splice site) | | 260 | 280 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 281 | 448 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 358 | 363 | MOTIF | ITIM motif 1. | might get lost (downstream of altered splice site) | | 360 | 360 | MOD_RES | Phosphotyrosine. | might get lost (downstream of altered splice site) | | 410 | 415 | MOTIF | ITIM motif 2. | might get lost (downstream of altered splice site) | | 440 | 445 | MOTIF | ITIM motif 3. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1347 / 1347 |
| position (AA) of stopcodon in wt / mu AA sequence | 449 / 449 |
| position of stopcodon in wt / mu cDNA | 1709 / 1709 |
| 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 | 363 / 363 |
| chromosome | 19 |
| strand | 1 |
| last intron/exon boundary | 1563 |
| theoretical NMD boundary in CDS | 1150 |
| length of CDS | 1347 |
| coding sequence (CDS) position | 13 |
cDNA position
(for ins/del: last normal base / first normal base) | 375 |
gDNA position
(for ins/del: last normal base / first normal base) | 19159 |
chromosomal position
(for ins/del: last normal base / first normal base) | 55174498 |
| original gDNA sequence snippet | GAGACGCCATGATCCCCACCTTCACGGCTCTGCTCTGCCTC |
| altered gDNA sequence snippet | GAGACGCCATGATCCCCACCCTCACGGCTCTGCTCTGCCTC |
| original cDNA sequence snippet | GAGACGCCATGATCCCCACCTTCACGGCTCTGCTCTGCCTC |
| altered cDNA sequence snippet | GAGACGCCATGATCCCCACCCTCACGGCTCTGCTCTGCCTC |
| wildtype AA sequence | MIPTFTALLC LGLSLGPRTH MQAGPLPKPT LWAEPGSVIS WGNSVTIWCQ GTLEAREYRL
DKEESPAPWD RQNPLEPKNK ARFSIPSMTE DYAGRYRCYY RSPVGWSQPS DPLELVMTGA
YSKPTLSALP SPLVTSGKSV TLLCQSRSPM DTFLLIKERA AHPLLHLRSE HGAQQHQAEF
PMSPVTSVHG GTYRCFSSHG FSHYLLSHPS DPLELIVSGS LEDPRPSPTR SVSTAAGPED
QPLMPTGSVP HSGLRRHWEV LIGVLVVSIL LLSLLLFLLL QHWRQGKHRT LAQRQADFQR
PPGAAEPEPK DGGLQRRSSP AADVQGENFC AAVKNTQPED GVEMDTRQSP HDEDPQAVTY
AKVKHSRPRR EMASPPSPLS GEFLDTKDRQ AEEDRQMDTE AAASEAPQDV TYAQLHSFTL
RQKATEPPPS QEGASPAEPS VYATLAIH* |
| mutated AA sequence | MIPTLTALLC LGLSLGPRTH MQAGPLPKPT LWAEPGSVIS WGNSVTIWCQ GTLEAREYRL
DKEESPAPWD RQNPLEPKNK ARFSIPSMTE DYAGRYRCYY RSPVGWSQPS DPLELVMTGA
YSKPTLSALP SPLVTSGKSV TLLCQSRSPM DTFLLIKERA AHPLLHLRSE HGAQQHQAEF
PMSPVTSVHG GTYRCFSSHG FSHYLLSHPS DPLELIVSGS LEDPRPSPTR SVSTAAGPED
QPLMPTGSVP HSGLRRHWEV LIGVLVVSIL LLSLLLFLLL QHWRQGKHRT LAQRQADFQR
PPGAAEPEPK DGGLQRRSSP AADVQGENFC AAVKNTQPED GVEMDTRQSP HDEDPQAVTY
AKVKHSRPRR EMASPPSPLS GEFLDTKDRQ AEEDRQMDTE AAASEAPQDV TYAQLHSFTL
RQKATEPPPS QEGASPAEPS VYATLAIH* |
| speed | 0.99 s |
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