Prediction |
polymorphism |
Model: simple_aae, prob: 0.999920512995644 (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) | chr21:18937758A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | CXADR |
| Ensembl transcript ID | ENST00000400165 |
| Genbank transcript ID | NM_001207064 |
| UniProt peptide | P78310 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.428A>G
cDNA.428A>G
g.53059A>G |
| AA changes | H143R Score: 29 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 143 |
| frameshift | no |
| known variant | Reference ID: rs437470
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 123 | 691 | 814 |
| ExAC | 1440 | 13961 | 15401 |
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 3.568 | 0.993 | | -3.017 | 0.038 | | (flanking) | 5.199 | 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 increased | 53050 | wt: 0.57 / mu: 0.72 | wt: AGGGAAGATGTGCCA
mu: AGGGAAGATGTGCCG | GGAA|gatg |
|
| distance from splice site | 13 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | |
| protein features | | start (aa) | end (aa) | feature | details | | | 20 | 237 | TOPO_DOM | Extracellular (Potential). | lost | | 141 | 228 | DOMAIN | Ig-like C2-type 2. | lost | | 145 | 148 | STRAND | | might get lost (downstream of altered splice site) | | 156 | 163 | STRAND | | might get lost (downstream of altered splice site) | | 162 | 162 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 166 | 168 | STRAND | | might get lost (downstream of altered splice site) | | 171 | 178 | STRAND | | might get lost (downstream of altered splice site) | | 185 | 192 | HELIX | | might get lost (downstream of altered splice site) | | 195 | 201 | STRAND | | might get lost (downstream of altered splice site) | | 201 | 201 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 208 | 215 | STRAND | | might get lost (downstream of altered splice site) | | 212 | 212 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 221 | 227 | STRAND | | might get lost (downstream of altered splice site) | | 238 | 258 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 259 | 259 | LIPID | S-palmitoyl cysteine (Probable). | might get lost (downstream of altered splice site) | | 259 | 260 | MUTAGEN | CC->AA: Loss of palmitoylation and altered localization. | might get lost (downstream of altered splice site) | | 259 | 365 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 260 | 260 | LIPID | S-palmitoyl cysteine (Probable). | might get lost (downstream of altered splice site) | | 293 | 293 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 300 | 300 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 306 | 306 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 318 | 318 | MUTAGEN | Y->A: Affects basolateral localization in airway epithelial cells. | might get lost (downstream of altered splice site) | | 323 | 323 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 332 | 332 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 345 | 348 | MUTAGEN | LSRM->AAAA: Affects basolateral localization in airway epithelial cells. | might get lost (downstream of altered splice site) | | 360 | 365 | MOTIF | PDZ-binding. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 603 / 603 |
| position (AA) of stopcodon in wt / mu AA sequence | 201 / 201 |
| position of stopcodon in wt / mu cDNA | 603 / 603 |
| 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 | 1 / 1 |
| chromosome | 21 |
| strand | 1 |
| last intron/exon boundary | 416 |
| theoretical NMD boundary in CDS | 365 |
| length of CDS | 603 |
| coding sequence (CDS) position | 428 |
cDNA position
(for ins/del: last normal base / first normal base) | 428 |
gDNA position
(for ins/del: last normal base / first normal base) | 53059 |
chromosomal position
(for ins/del: last normal base / first normal base) | 18937758 |
| original gDNA sequence snippet | CTTTGCAGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC |
| altered gDNA sequence snippet | CTTTGCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC |
| original cDNA sequence snippet | AGTTCTTGGGAAGATGTGCCACCTCCAAAGAGCCGTACGTC |
| altered cDNA sequence snippet | AGTTCTTGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTC |
| wildtype AA sequence | MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLGK MCHLQRAVRP LPEATSAVII HPWGPCLLPT WKDIPRLSIT
KYQVKTLNAL LRVRLSHLLR * |
| mutated AA sequence | MALLLCFVLL CGVVDFARSL SITTPEEMIE KAKGETAYLP CKFTLSPEDQ GPLDIEWLIS
PADNQKVDQV IILYSGDKIY DDYYPDLKGR VHFTSNDLKS GDASINVTNL QLSDIGTYQC
KVKKAPGVAN KKIHLVVLGK MCRLQRAVRP LPEATSAVII HPWGPCLLPT WKDIPRLSIT
KYQVKTLNAL LRVRLSHLLR * |
| speed | 0.82 s |
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