Prediction |
polymorphism |
Model: simple_aae, prob: 1 (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 CM116474)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr6:16145325A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | MYLIP |
| Ensembl transcript ID | ENST00000349606 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q8WY64 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.482A>G
cDNA.986A>G
g.15970A>G |
| AA changes | N161S Score: 46 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 161 |
| frameshift | no |
| known variant | Reference ID: rs9370867
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 1583 | 690 | 2273 |
| ExAC | 24045 | -15323 | 8722 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM116474)
|
| regulatory features | PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.087 | 0 | | 1.532 | 0.002 | | (flanking) | -0.605 | 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 increased | 15961 | wt: 0.74 / mu: 0.87 | wt: CCTCGTTTCAAGAAA
mu: CCTCGTTTCAAGAAG | TCGT|ttca | | Acc gained | 15966 | 0.38 | mu: GCGTTGTGGACCTCGTTTCAAGAAGCAACCAGAGCCCTTCA | tcaa|GAAG | | Donor gained | 15969 | 0.91 | mu: CAAGAAGCAACCAGA | AGAA|gcaa | | Donor gained | 15964 | 0.63 | mu: CGTTTCAAGAAGCAA | TTTC|aaga |
|
| distance from splice site | 198 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 161 | Y | N | A | G | V | V | D | L | V | S | R | N | N | Q | S | P | S | H | S | P | L | K | S | S |
| mutated | all conserved | | 161 | Y | N | A | G | V | V | D | L | V | S | R | S | N | Q | S | P | S | H | S | P | L | K | S |
| Ptroglodytes | all conserved | ENSPTRG00000023743 | 342 | Y | N | A | G | V | V | D | L | V | S | R | S | N | Q | S | P | S | H | S | P | L | K | S |
| Mmulatta | all conserved | ENSMMUG00000015474 | 342 | Y | N | A | G | V | V | D | L | V | S | R | S | N | Q | S | P | S | H | S | P | L | K | S |
| Fcatus | all conserved | ENSFCAG00000010500 | 313 | | | | | | | | | | | | S | D | P | S | P | P | N | S | P | L | K | S |
| Mmusculus | all conserved | ENSMUSG00000038175 | 342 | Y | N | A | G | V | V | D | L | V | S | R | S | D | Q | S | P | P | S | S | P | L | K | S |
| Ggallus | all conserved | ENSGALG00000012704 | 314 | Y | N | A | G | I | V | D | L | V | S | R | S | D | Q | T | P | P | S | S | P | L | K | S |
| Trubripes | no homologue | | | |
| Drerio | not conserved | ENSDARG00000008859 | 342 | Y | N | A | G | I | V | D | M | M | S | RP | G | E | R | T | P | S | NR | S | P | S | R | E |
| Dmelanogaster | not conserved | FBgn0260866 | 482 | H | E | R | G | - | G | D | L | V | A | E | G | A | EGCSAVAGGLGASAVG | | | | | | | | | |
| Celegans | no homologue | | | |
| Xtropicalis | all conserved | ENSXETG00000015431 | 342 | Y | N | A | G | I | V | D | L | V | S | G | S | G | H | S | E | P | S | S | P | L | K | T |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 279 | DOMAIN | FERM. | lost | | 199 | 199 | CONFLICT | K -> R (in Ref. 1; AAF18974). | might get lost (downstream of altered splice site) | | 262 | 263 | CONFLICT | SG -> TR (in Ref. 3; AAF87323). | might get lost (downstream of altered splice site) | | 265 | 265 | MUTAGEN | Y->A: Unable to clear LDLR from the plasma membrane. | might get lost (downstream of altered splice site) | | 269 | 269 | MUTAGEN | T->R: Unable to clear LDLR from the plasma membrane. | might get lost (downstream of altered splice site) | | 309 | 310 | CONFLICT | KK -> PRN (in Ref. 3; AAF87323). | might get lost (downstream of altered splice site) | | 360 | 360 | METAL | Iron. | might get lost (downstream of altered splice site) | | 363 | 363 | METAL | Iron. | might get lost (downstream of altered splice site) | | 368 | 368 | METAL | Iron. | might get lost (downstream of altered splice site) | | 374 | 384 | HELIX | | might get lost (downstream of altered splice site) | | 387 | 387 | MUTAGEN | C->A: Abolishes ubiquitin ligase activity. | might get lost (downstream of altered splice site) | | 387 | 387 | MUTAGEN | C->A: Abolishes autoubiquitination. | might get lost (downstream of altered splice site) | | 387 | 422 | ZN_FING | RING-type. | might get lost (downstream of altered splice site) | | 388 | 390 | TURN | | might get lost (downstream of altered splice site) | | 389 | 389 | MUTAGEN | V->R: Inhibits LDLR degradation. | might get lost (downstream of altered splice site) | | 391 | 394 | STRAND | | might get lost (downstream of altered splice site) | | 397 | 400 | STRAND | | might get lost (downstream of altered splice site) | | 409 | 412 | HELIX | | might get lost (downstream of altered splice site) | | 415 | 415 | MUTAGEN | L->E: Inhibits LDLR degradation. | might get lost (downstream of altered splice site) | | 419 | 421 | TURN | | might get lost (downstream of altered splice site) | | 427 | 430 | STRAND | | might get lost (downstream of altered splice site) | | 431 | 433 | REGION | Critical for homodimerization. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 795 / 795 |
| position (AA) of stopcodon in wt / mu AA sequence | 265 / 265 |
| position of stopcodon in wt / mu cDNA | 1299 / 1299 |
| 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 | 505 / 505 |
| chromosome | 6 |
| strand | 1 |
| last intron/exon boundary | 1210 |
| theoretical NMD boundary in CDS | 655 |
| length of CDS | 795 |
| coding sequence (CDS) position | 482 |
cDNA position
(for ins/del: last normal base / first normal base) | 986 |
gDNA position
(for ins/del: last normal base / first normal base) | 15970 |
chromosomal position
(for ins/del: last normal base / first normal base) | 16145325 |
| original gDNA sequence snippet | TGTGGACCTCGTTTCAAGAAACAACCAGAGCCCTTCACACT |
| altered gDNA sequence snippet | TGTGGACCTCGTTTCAAGAAGCAACCAGAGCCCTTCACACT |
| original cDNA sequence snippet | TGTGGACCTCGTTTCAAGAAACAACCAGAGCCCTTCACACT |
| altered cDNA sequence snippet | TGTGGACCTCGTTTCAAGAAGCAACCAGAGCCCTTCACACT |
| wildtype AA sequence | MENYGIEWHS VRDSEGQKLL IGVGPEGISI CKDDFSPINR IAYPVVQMAT QSGKNVYLTV
TKESGNSIVL LFKMISTRAA SGLYRAITET HAFYRCDTVT SAVMMQYSRD LKGHLASLFL
NENINLGKKY VFDIKRTSKE VYDHARRALY NAGVVDLVSR NNQSPSHSPL KSSESSMNCS
SCEGLSCQQT RVLQEKLRKL KEAMLCMVCC EEEINSTFCP CGHTVCCESC AAQLQSCPVC
RSRVEHVQHV YLPTHTSLLN LTVI* |
| mutated AA sequence | MENYGIEWHS VRDSEGQKLL IGVGPEGISI CKDDFSPINR IAYPVVQMAT QSGKNVYLTV
TKESGNSIVL LFKMISTRAA SGLYRAITET HAFYRCDTVT SAVMMQYSRD LKGHLASLFL
NENINLGKKY VFDIKRTSKE VYDHARRALY NAGVVDLVSR SNQSPSHSPL KSSESSMNCS
SCEGLSCQQT RVLQEKLRKL KEAMLCMVCC EEEINSTFCP CGHTVCCESC AAQLQSCPVC
RSRVEHVQHV YLPTHTSLLN LTVI* |
| speed | 1.48 s |
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