Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999651627 (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) | chr1:236706862G>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | LGALS8 |
| Ensembl transcript ID | ENST00000416919 |
| Genbank transcript ID | N/A |
| UniProt peptide | O00214 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.501G>C
cDNA.646G>C
g.25563G>C |
| AA changes | R167S Score: 110 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 167 |
| frameshift | no |
| known variant | Reference ID: rs2243525
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 1169 | 1056 | 2225 |
| ExAC | 31626 | -30485 | 1141 |
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.117 | 0.201 | | -1.301 | 0.105 | | (flanking) | 1.327 | 0.886 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | alteration within used splice site, likely to disturb normal splicing
| effect | gDNA position | score | detection sequence | exon-intron border | | Acceptor lost | 25560 | sequence motif lost | - | wt: tcag|AGGC
mu: tcag.AGCC | | Acc increased | 25572 | wt: 0.42 / mu: 0.70 | wt: TCTTTTCAGAGGCTGCCATTCGCTGCAAGGTTGAACACCCC
mu: TCTTTTCAGAGCCTGCCATTCGCTGCAAGGTTGAACACCCC | attc|GCTG | | Acc gained | 25565 | 0.35 | mu: TGTGGCTTCTTTTCAGAGCCTGCCATTCGCTGCAAGGTTGA | gcct|GCCA |
|
| distance from splice site | 3 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 167 | T | K | I | P | P | M | N | Y | V | S | K | R | L | P | F | A | A | R | L | N | T | P | M | G |
| mutated | not conserved | | 167 | T | K | I | P | P | M | N | Y | V | S | K | S | L | P | F | A | A | R | L | N | T | P | M |
| Ptroglodytes | all conserved | ENSPTRG00000002140 | 193 | S | K | I | A | P | R | T | V | Y | T | KSKDSTVNHTLTCT | K | I | PPMNCVSKSLP | F | A | A | R | L | N | T | P | M |
| Mmulatta | not conserved | ENSMMUG00000015132 | 188 | | | | PQL | P | S | N | RGD | I | S | K | I | V | PRTVYTKSKDSTVNHSLTCTKIPPMNYVSKSLP | F | A | A | R | L | N | T | P | M |
| Fcatus | not conserved | ENSFCAG00000003385 | 188 | | | | SQFPSNRGDISKIVPRTVYTKSKGSTANHSLTCAKIL | P | T | N | C | L | S | K | T | L | P | F | V | A | R | L | N | S | S | M |
| Mmusculus | not conserved | ENSMUSG00000057554 | 187 | | | | | | E | N | IQKPGK | L | Q | L | S | L | P | F | E | A | R | L | N | A | S | M |
| Ggallus | not conserved | ENSGALG00000014371 | 184 | | | | | | | | | F | - | E | G | V | P | Y | V | G | K | L | V | S | A | L |
| Trubripes | no homologue | | | |
| Drerio | not conserved | ENSDARG00000037066 | 166 | S | E | S | K | K | E | N | Q | L | Q | F | H | L | P | F | R | S | K | L | A | K | G | L |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | all conserved | ENSXETG00000009015 | 165 | T | I | LGS | Q | P | T | S | F | AVNSIEGNQGR | S | E | K | LLTFSV | P | Y | T | | | | | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 171 | 171 | CONFLICT | S -> V (in Ref. 1; AAB51605). | might get lost (downstream of altered splice site) | | 185 | 193 | STRAND | | might get lost (downstream of altered splice site) | | 187 | 317 | DOMAIN | Galectin 2. | might get lost (downstream of altered splice site) | | 199 | 199 | CONFLICT | R -> G (in Ref. 8; AAL77076). | might get lost (downstream of altered splice site) | | 200 | 207 | STRAND | | might get lost (downstream of altered splice site) | | 204 | 204 | CONFLICT | K -> Q (in Ref. 1; AAB51605). | might get lost (downstream of altered splice site) | | 213 | 220 | STRAND | | might get lost (downstream of altered splice site) | | 221 | 224 | TURN | | might get lost (downstream of altered splice site) | | 225 | 225 | CONFLICT | D -> H (in Ref. 8; AAL77076). | might get lost (downstream of altered splice site) | | 225 | 233 | STRAND | | might get lost (downstream of altered splice site) | | 234 | 237 | TURN | | might get lost (downstream of altered splice site) | | 238 | 244 | STRAND | | might get lost (downstream of altered splice site) | | 246 | 249 | STRAND | | might get lost (downstream of altered splice site) | | 249 | 255 | REGION | Beta-galactoside binding (By similarity). | might get lost (downstream of altered splice site) | | 256 | 258 | STRAND | | might get lost (downstream of altered splice site) | | 259 | 259 | CONFLICT | F -> L (in Ref. 7; AAK16736). | might get lost (downstream of altered splice site) | | 266 | 273 | STRAND | | might get lost (downstream of altered splice site) | | 275 | 282 | STRAND | | might get lost (downstream of altered splice site) | | 285 | 291 | STRAND | | might get lost (downstream of altered splice site) | | 297 | 299 | HELIX | | might get lost (downstream of altered splice site) | | 302 | 315 | STRAND | | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 903 / 903 |
| position (AA) of stopcodon in wt / mu AA sequence | 301 / 301 |
| position of stopcodon in wt / mu cDNA | 1048 / 1048 |
| 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 | 146 / 146 |
| chromosome | 1 |
| strand | 1 |
| last intron/exon boundary | 899 |
| theoretical NMD boundary in CDS | 703 |
| length of CDS | 903 |
| coding sequence (CDS) position | 501 |
cDNA position
(for ins/del: last normal base / first normal base) | 646 |
gDNA position
(for ins/del: last normal base / first normal base) | 25563 |
chromosomal position
(for ins/del: last normal base / first normal base) | 236706862 |
| original gDNA sequence snippet | ACTGTGGCTTCTTTTCAGAGGCTGCCATTCGCTGCAAGGTT |
| altered gDNA sequence snippet | ACTGTGGCTTCTTTTCAGAGCCTGCCATTCGCTGCAAGGTT |
| original cDNA sequence snippet | ATGAACTATGTGTCAAAGAGGCTGCCATTCGCTGCAAGGTT |
| altered cDNA sequence snippet | ATGAACTATGTGTCAAAGAGCCTGCCATTCGCTGCAAGGTT |
| wildtype AA sequence | MMLSLNNLQN IIYNPVIPFV GTIPDQLDPG TLIVIRGHVP SDADRFQVDL QNGSSMKPRA
DVAFHFNPRF KRAGCIVCNT LINEKWGREE ITYDTPFKRE KSFEIVIMVL KDKFQVPKSG
TPQLPSNRGG DISKIAPRTV YTKSKDSTVN HTLTCTKIPP MNYVSKRLPF AARLNTPMGP
GRTVVVKGEV NANAKSFNVD LLAGKSKDIA LHLNPRLNIK AFVRNSFLQE SWGEEERNIT
SFPFSPGMYF EMIIYCDVRE FKVAVNGVHS LEYKHRFKEL SSIDTLEING DIHLLEVRSW
* |
| mutated AA sequence | MMLSLNNLQN IIYNPVIPFV GTIPDQLDPG TLIVIRGHVP SDADRFQVDL QNGSSMKPRA
DVAFHFNPRF KRAGCIVCNT LINEKWGREE ITYDTPFKRE KSFEIVIMVL KDKFQVPKSG
TPQLPSNRGG DISKIAPRTV YTKSKDSTVN HTLTCTKIPP MNYVSKSLPF AARLNTPMGP
GRTVVVKGEV NANAKSFNVD LLAGKSKDIA LHLNPRLNIK AFVRNSFLQE SWGEEERNIT
SFPFSPGMYF EMIIYCDVRE FKVAVNGVHS LEYKHRFKEL SSIDTLEING DIHLLEVRSW
* |
| speed | 1.21 s |
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