Prediction |
disease causing |
Model: simple_aae, prob: 0.999800507292538 (classification due to ClinVar,
real probability is shown anyway)
(explain) |
| Summary |
- amino acid sequence changed
- known disease mutation at this position (HGMD CM910174)
- known disease mutation: rs4316 (pathogenic)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr1:155206217G>AN/A
show variant in all transcripts IGV
|
| HGNC symbol | GBA |
| Ensembl transcript ID | ENST00000428024 |
| Genbank transcript ID | NM_001171811 |
| UniProt peptide | P04062 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.782C>T
cDNA.1285C>T
g.8437C>T |
| AA changes | A261V Score: 64 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 261 |
| frameshift | no |
| known variant | Reference ID: rs78396650
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4316 (pathogenic for Gaucher's disease, type 1) dbSNP
NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.057 | 0.996 | | 2.663 | 1 | | (flanking) | 4.346 | 0.999 |
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 increased | 8446 | wt: 0.37 / mu: 0.59 | wt: TCATGGCATTGCTGTACATTGGTACCTGGACTTTCTGGCTC
mu: TCATGGCATTGTTGTACATTGGTACCTGGACTTTCTGGCTC | attg|GTAC | | Acc increased | 8442 | wt: 0.31 / mu: 0.42 | wt: ATGTTCATGGCATTGCTGTACATTGGTACCTGGACTTTCTG
mu: ATGTTCATGGCATTGTTGTACATTGGTACCTGGACTTTCTG | gtac|ATTG |
|
| distance from splice site | 44 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 261 | D | P | E | A | A | K | Y | V | H | G | I | A | V | H | W | Y | L | D | F | L | A | P | A | K |
| mutated | not conserved | | 261 | D | P | E | A | A | K | Y | V | H | G | I | V | V | H | W | Y | L | D | F | L | A | P | A |
| Ptroglodytes | all identical | ENSPTRG00000001416 | 348 | D | P | E | A | A | K | Y | V | H | G | I | A | V | H | W | Y | L | D | F | L | A | P | A |
| Mmulatta | no homologue | | | |
| Fcatus | no homologue | | | |
| Mmusculus | all identical | ENSMUSG00000028048 | 327 | D | P | E | A | A | K | Y | V | H | G | I | A | V | H | W | Y | M | D | F | L | A | P | A |
| Ggallus | no homologue | | | |
| Trubripes | all identical | ENSTRUG00000010884 | 334 | D | V | H | A | G | R | Y | V | H | G | V | A | V | H | W | Y | M | D | S | L | V | P | A |
| Drerio | not conserved | ENSDARG00000076058 | 330 | D | I | K | A | A | R | Y | V | H | G | I | G | V | H | W | Y | F | D | R | L | V | P | P |
| Dmelanogaster | all conserved | FBgn0051148 | 375 | | | | | I | D | Y | L | D | G | L | S | L | H | W | Y | W | D | E | I | F | - | G |
| Celegans | all identical | Y4C6B.6 | 330 | D | P | T | A | A | Q | Y | V | H | G | I | A | I | H | | | | | | | | | |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 243 | 261 | HELIX | | lost | | 267 | 271 | STRAND | | might get lost (downstream of altered splice site) | | 274 | 274 | ACT_SITE | Proton donor. | might get lost (downstream of altered splice site) | | 275 | 279 | HELIX | | might get lost (downstream of altered splice site) | | 284 | 286 | STRAND | | might get lost (downstream of altered splice site) | | 292 | 301 | HELIX | | might get lost (downstream of altered splice site) | | 303 | 308 | HELIX | | might get lost (downstream of altered splice site) | | 309 | 309 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 311 | 314 | TURN | | might get lost (downstream of altered splice site) | | 315 | 323 | STRAND | | might get lost (downstream of altered splice site) | | 324 | 326 | HELIX | | might get lost (downstream of altered splice site) | | 329 | 335 | HELIX | | might get lost (downstream of altered splice site) | | 338 | 341 | HELIX | | might get lost (downstream of altered splice site) | | 346 | 352 | STRAND | | might get lost (downstream of altered splice site) | | 354 | 356 | HELIX | | might get lost (downstream of altered splice site) | | 359 | 369 | HELIX | | might get lost (downstream of altered splice site) | | 373 | 381 | STRAND | | might get lost (downstream of altered splice site) | | 379 | 379 | MUTAGEN | E->G: Decreases activity 1000-fold. | might get lost (downstream of altered splice site) | | 379 | 379 | ACT_SITE | Nucleophile. | might get lost (downstream of altered splice site) | | 386 | 388 | STRAND | | might get lost (downstream of altered splice site) | | 396 | 411 | HELIX | | might get lost (downstream of altered splice site) | | 414 | 424 | STRAND | | might get lost (downstream of altered splice site) | | 426 | 428 | STRAND | | might get lost (downstream of altered splice site) | | 440 | 444 | STRAND | | might get lost (downstream of altered splice site) | | 445 | 447 | HELIX | | might get lost (downstream of altered splice site) | | 449 | 452 | STRAND | | might get lost (downstream of altered splice site) | | 454 | 463 | HELIX | | might get lost (downstream of altered splice site) | | 470 | 470 | CONFLICT | S -> I (in Ref. 15; AA sequence). | might get lost (downstream of altered splice site) | | 471 | 479 | STRAND | | might get lost (downstream of altered splice site) | | 482 | 489 | STRAND | | might get lost (downstream of altered splice site) | | 495 | 501 | STRAND | | might get lost (downstream of altered splice site) | | 501 | 501 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 503 | 505 | STRAND | | might get lost (downstream of altered splice site) | | 507 | 513 | STRAND | | might get lost (downstream of altered splice site) | | 514 | 516 | TURN | | might get lost (downstream of altered splice site) | | 517 | 523 | STRAND | | might get lost (downstream of altered splice site) | | 527 | 533 | STRAND | | might get lost (downstream of altered splice site) | | 534 | 534 | CONFLICT | R -> H (in Ref. 1; AAA35873). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1350 / 1350 |
| position (AA) of stopcodon in wt / mu AA sequence | 450 / 450 |
| position of stopcodon in wt / mu cDNA | 1853 / 1853 |
| 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 | 504 / 504 |
| chromosome | 1 |
| strand | -1 |
| last intron/exon boundary | 1748 |
| theoretical NMD boundary in CDS | 1194 |
| length of CDS | 1350 |
| coding sequence (CDS) position | 782 |
cDNA position
(for ins/del: last normal base / first normal base) | 1285 |
gDNA position
(for ins/del: last normal base / first normal base) | 8437 |
chromosomal position
(for ins/del: last normal base / first normal base) | 155206217 |
| original gDNA sequence snippet | TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT |
| altered gDNA sequence snippet | TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT |
| original cDNA sequence snippet | TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT |
| altered cDNA sequence snippet | TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT |
| wildtype AA sequence | MELSMGPIQA NHTGTGLLLT LQPEQKFQKV KGFGGAMTDA AALNILALSP PAQNLLLKSY
FSEEGIGYNI IRVPMASCDF SIRTYTYADT PDDFQLHNFS LPEEDTKLKI PLIHRALQLA
QRPVSLLASP WTSPTWLKTN GAVNGKGSLK GQPGDIYHQT WARYFVKFLD AYAEHKLQFW
AVTAENEPSA GLLSGYPFQC LGFTPEHQRD FIARDLGPTL ANSTHHNVRL LMLDDQRLLL
PHWAKVVLTD PEAAKYVHGI AVHWYLDFLA PAKATLGETH RLFPNTMLFA SEACVGSKFW
EQSVRLGSWD RGMQYSHSII TNLLYHVVGW TDWNLALNPE GGPNWVRNFV DSPIIVDITK
DTFYKQPMFY HLGHFSKFIP EGSQRVGLVA SQKNDLDAVA LMHPDGSAVV VVLNRSSKDV
PLTIKDPAVG FLETISPGYS IHTYLWRRQ* |
| mutated AA sequence | MELSMGPIQA NHTGTGLLLT LQPEQKFQKV KGFGGAMTDA AALNILALSP PAQNLLLKSY
FSEEGIGYNI IRVPMASCDF SIRTYTYADT PDDFQLHNFS LPEEDTKLKI PLIHRALQLA
QRPVSLLASP WTSPTWLKTN GAVNGKGSLK GQPGDIYHQT WARYFVKFLD AYAEHKLQFW
AVTAENEPSA GLLSGYPFQC LGFTPEHQRD FIARDLGPTL ANSTHHNVRL LMLDDQRLLL
PHWAKVVLTD PEAAKYVHGI VVHWYLDFLA PAKATLGETH RLFPNTMLFA SEACVGSKFW
EQSVRLGSWD RGMQYSHSII TNLLYHVVGW TDWNLALNPE GGPNWVRNFV DSPIIVDITK
DTFYKQPMFY HLGHFSKFIP EGSQRVGLVA SQKNDLDAVA LMHPDGSAVV VVLNRSSKDV
PLTIKDPAVG FLETISPGYS IHTYLWRRQ* |
| speed | 0.79 s |
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