Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999999999 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- amino acid sequence changed
- homozygous in TGP or ExAC
- known disease mutation at this position (HGMD CM176333)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr14:94847415A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | SERPINA1 |
| Ensembl transcript ID | ENST00000449399 |
| Genbank transcript ID | N/A |
| UniProt peptide | P01009 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.710T>C
cDNA.1012T>C
g.9616T>C |
| AA changes | V237A Score: 64 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 237 |
| frameshift | no |
| known variant | Reference ID: rs6647
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 298 | 653 | 951 |
| ExAC | 3906 | 18922 | 22828 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM176333)
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -1.376 | 0.001 | | -1.01 | 0 | | (flanking) | -1.031 | 0 |
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 | 9614 | wt: 0.5398 / mu: 0.5844 (marginal change - not scored) | wt: GACCAGGTGACCACC
mu: GACCAGGCGACCACC | CCAG|gtga | | Donor increased | 9613 | wt: 0.70 / mu: 0.89 | wt: GGACCAGGTGACCAC
mu: GGACCAGGCGACCAC | ACCA|ggtg |
|
| distance from splice site | 64 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 237 | D | T | E | E | E | D | F | H | V | D | Q | V | T | T | V | K | V | P | M | M | K | R | L | G |
| mutated | not conserved | | 237 | D | T | E | E | E | D | F | H | V | D | Q | A | T | T | V | | | | | | | | |
| Ptroglodytes | not conserved | ENSPTRG00000023666 | 237 | D | T | E | E | E | D | F | H | V | D | Q | A | T | T | V | | | | | | | | |
| Mmulatta | not conserved | ENSMMUG00000020426 | 237 | A | T | K | E | E | D | F | H | V | D | Q | A | T | T | V | | | | | | | | |
| Fcatus | no homologue | | | |
| Mmusculus | not conserved | ENSMUSG00000021081 | 231 | S | V | K | V | K | D | Y | H | L | G | Y | G | M | T | | | | | | | | | |
| Ggallus | not conserved | ENSGALG00000010969 | 238 | N | T | E | E | R | E | F | F | V | D | A | E | T | T | V | K | V | P | M | M | C | R | |
| Trubripes | no homologue | | | |
| Drerio | no homologue | | | |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | not conserved | ENSXETG00000023329 | 257 | F | T | Q | D | G | I | F | H | V | D | E | N | T | N | V | T | V | P | M | M | R | R | N |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 238 | 256 | STRAND | | might get lost (downstream of altered splice site) | | 256 | 256 | MOD_RES | S-cysteinyl cysteine. | might get lost (downstream of altered splice site) | | 257 | 260 | TURN | | might get lost (downstream of altered splice site) | | 261 | 268 | STRAND | | might get lost (downstream of altered splice site) | | 269 | 271 | TURN | | might get lost (downstream of altered splice site) | | 271 | 271 | CARBOHYD | N-linked (GlcNAc...) (complex). | might get lost (downstream of altered splice site) | | 272 | 279 | STRAND | | might get lost (downstream of altered splice site) | | 273 | 273 | CONFLICT | T -> N (in Ref. 1; AAB59375). | might get lost (downstream of altered splice site) | | 280 | 280 | CONFLICT | D -> G (in Ref. 7; ABG73380). | might get lost (downstream of altered splice site) | | 280 | 282 | STRAND | | might get lost (downstream of altered splice site) | | 284 | 290 | HELIX | | might get lost (downstream of altered splice site) | | 293 | 301 | HELIX | | might get lost (downstream of altered splice site) | | 306 | 313 | STRAND | | might get lost (downstream of altered splice site) | | 315 | 322 | STRAND | | might get lost (downstream of altered splice site) | | 323 | 329 | HELIX | | might get lost (downstream of altered splice site) | | 326 | 326 | CONFLICT | V -> I (in Ref. 3; CAA25838). | might get lost (downstream of altered splice site) | | 334 | 336 | HELIX | | might get lost (downstream of altered splice site) | | 337 | 340 | STRAND | | might get lost (downstream of altered splice site) | | 343 | 345 | TURN | | might get lost (downstream of altered splice site) | | 346 | 349 | STRAND | | might get lost (downstream of altered splice site) | | 355 | 364 | STRAND | | might get lost (downstream of altered splice site) | | 366 | 371 | STRAND | | might get lost (downstream of altered splice site) | | 368 | 392 | REGION | RCL. | might get lost (downstream of altered splice site) | | 374 | 376 | HELIX | | might get lost (downstream of altered splice site) | | 375 | 418 | PEPTIDE | Short peptide from AAT. /FTId=PRO_0000364030. | might get lost (downstream of altered splice site) | | 379 | 383 | STRAND | | might get lost (downstream of altered splice site) | | 382 | 382 | MUTAGEN | M->V: Oxidation-resistant inhibitor of therapeutic importance. | might get lost (downstream of altered splice site) | | 382 | 383 | SITE | Reactive bond. | might get lost (downstream of altered splice site) | | 387 | 389 | STRAND | | might get lost (downstream of altered splice site) | | 394 | 400 | STRAND | | might get lost (downstream of altered splice site) | | 401 | 403 | TURN | | might get lost (downstream of altered splice site) | | 406 | 413 | STRAND | | might get lost (downstream of altered splice site) | | 410 | 410 | CONFLICT | G -> L (in Ref. 24; AA sequence). | might get lost (downstream of altered splice site) | | 414 | 414 | CONFLICT | N -> S (in Ref. 24; AA sequence). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1257 / 1257 |
| position (AA) of stopcodon in wt / mu AA sequence | 419 / 419 |
| position of stopcodon in wt / mu cDNA | 1559 / 1559 |
| 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 | 303 / 303 |
| chromosome | 14 |
| strand | -1 |
| last intron/exon boundary | 1368 |
| theoretical NMD boundary in CDS | 1015 |
| length of CDS | 1257 |
| coding sequence (CDS) position | 710 |
cDNA position
(for ins/del: last normal base / first normal base) | 1012 |
gDNA position
(for ins/del: last normal base / first normal base) | 9616 |
chromosomal position
(for ins/del: last normal base / first normal base) | 94847415 |
| original gDNA sequence snippet | GGACTTCCACGTGGACCAGGTGACCACCGTGAAGGTGCCTA |
| altered gDNA sequence snippet | GGACTTCCACGTGGACCAGGCGACCACCGTGAAGGTGCCTA |
| original cDNA sequence snippet | GGACTTCCACGTGGACCAGGTGACCACCGTGAAGGTGCCTA |
| altered cDNA sequence snippet | GGACTTCCACGTGGACCAGGCGACCACCGTGAAGGTGCCTA |
| wildtype AA sequence | MPSSVSWGIL LLAGLCCLVP VSLAEDPQGD AAQKTDTSHH DQDHPTFNKI TPNLAEFAFS
LYRQLAHQSN STNIFFSPVS IATAFAMLSL GTKADTHDEI LEGLNFNLTE IPEAQIHEGF
QELLRTLNQP DSQLQLTTGN GLFLSEGLKL VDKFLEDVKK LYHSEAFTVN FGDTEEAKKQ
INDYVEKGTQ GKIVDLVKEL DRDTVFALVN YIFFKGKWER PFEVKDTEEE DFHVDQVTTV
KVPMMKRLGM FNIQHCKKLS SWVLLMKYLG NATAIFFLPD EGKLQHLENE LTHDIITKFL
ENEDRRSASL HLPKLSITGT YDLKSVLGQL GITKVFSNGA DLSGVTEEAP LKLSKAVHKA
VLTIDEKGTE AAGAMFLEAI PMSIPPEVKF NKPFVFLMIE QNTKSPLFMG KVVNPTQK* |
| mutated AA sequence | MPSSVSWGIL LLAGLCCLVP VSLAEDPQGD AAQKTDTSHH DQDHPTFNKI TPNLAEFAFS
LYRQLAHQSN STNIFFSPVS IATAFAMLSL GTKADTHDEI LEGLNFNLTE IPEAQIHEGF
QELLRTLNQP DSQLQLTTGN GLFLSEGLKL VDKFLEDVKK LYHSEAFTVN FGDTEEAKKQ
INDYVEKGTQ GKIVDLVKEL DRDTVFALVN YIFFKGKWER PFEVKDTEEE DFHVDQATTV
KVPMMKRLGM FNIQHCKKLS SWVLLMKYLG NATAIFFLPD EGKLQHLENE LTHDIITKFL
ENEDRRSASL HLPKLSITGT YDLKSVLGQL GITKVFSNGA DLSGVTEEAP LKLSKAVHKA
VLTIDEKGTE AAGAMFLEAI PMSIPPEVKF NKPFVFLMIE QNTKSPLFMG KVVNPTQK* |
| speed | 0.77 s |
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