Prediction |
polymorphism |
Model: without_aae, prob: 0.999978082375069 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- 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) | chr17:48610272G>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | EPN3 |
| Ensembl transcript ID | ENST00000268933 |
| Genbank transcript ID | NM_017957 |
| UniProt peptide | Q9H201 |
| alteration type | single base exchange |
| alteration region | 5'UTR |
| DNA changes | cDNA.369G>C
g.369G>C |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs755046
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 1643 | 742 | 2385 |
| ExAC | 3142 | 1902 | 5044 |
|
| regulatory features | CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.396 | 0.003 | | -0.089 | 0 | | (flanking) | 0.01 | 0 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | splice site change before start ATG (at aa -69) | splice site change before start ATG (at aa -68) | splice site change before start ATG (at aa -67) | | effect | gDNA position | score | detection sequence | exon-intron border | | Acc increased | 376 | wt: 0.46 / mu: 0.82 | wt: GCTGTGCCGTCCCGCTGCTGCACAGGTCGGAGGGTCACCGC
mu: GCTGTGCCGTCCCCCTGCTGCACAGGTCGGAGGGTCACCGC | ctgc|ACAG | | Acc increased | 378 | wt: 0.51 / mu: 0.80 | wt: TGTGCCGTCCCGCTGCTGCACAGGTCGGAGGGTCACCGCAG
mu: TGTGCCGTCCCCCTGCTGCACAGGTCGGAGGGTCACCGCAG | gcac|AGGT | | Acc marginally increased | 370 | wt: 0.2597 / mu: 0.2776 (marginal change - not scored) | wt: CCCGAGGCTGTGCCGTCCCGCTGCTGCACAGGTCGGAGGGT
mu: CCCGAGGCTGTGCCGTCCCCCTGCTGCACAGGTCGGAGGGT | ccgc|TGCT | | Acc increased | 375 | wt: 0.39 / mu: 0.78 | wt: GGCTGTGCCGTCCCGCTGCTGCACAGGTCGGAGGGTCACCG
mu: GGCTGTGCCGTCCCCCTGCTGCACAGGTCGGAGGGTCACCG | gctg|CACA | | Acc marginally increased | 380 | wt: 0.9016 / mu: 0.9573 (marginal change - not scored) | wt: TGCCGTCCCGCTGCTGCACAGGTCGGAGGGTCACCGCAGAG
mu: TGCCGTCCCCCTGCTGCACAGGTCGGAGGGTCACCGCAGAG | acag|GTCG | | Acc gained | 371 | 0.77 | mu: CCGAGGCTGTGCCGTCCCCCTGCTGCACAGGTCGGAGGGTC | ccct|GCTG | | Donor gained | 374 | 0.36 | mu: CCTGCTGCACAGGTC | TGCT|gcac |
|
| distance from splice site | 75 |
| Kozak consensus sequence altered? | no |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 8 | 8 | BINDING | Phosphatidylinositol lipid headgroup (By similarity). | might get lost (downstream of altered splice site) | | 11 | 11 | BINDING | Phosphatidylinositol lipid headgroup (By similarity). | might get lost (downstream of altered splice site) | | 12 | 144 | DOMAIN | ENTH. | might get lost (downstream of altered splice site) | | 17 | 17 | MOD_RES | Phosphotyrosine. | might get lost (downstream of altered splice site) | | 25 | 25 | BINDING | Phosphatidylinositol lipid headgroup (By similarity). | might get lost (downstream of altered splice site) | | 30 | 30 | BINDING | Phosphatidylinositol lipid headgroup (By similarity). | might get lost (downstream of altered splice site) | | 63 | 63 | BINDING | Phosphatidylinositol lipid headgroup (By similarity). | might get lost (downstream of altered splice site) | | 73 | 73 | BINDING | Phosphatidylinositol lipid headgroup (By similarity). | might get lost (downstream of altered splice site) | | 176 | 176 | MOD_RES | Phosphotyrosine. | might get lost (downstream of altered splice site) | | 182 | 182 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 186 | 186 | MOD_RES | Phosphotyrosine. | might get lost (downstream of altered splice site) | | 209 | 228 | REPEAT | UIM 1. | might get lost (downstream of altered splice site) | | 236 | 255 | REPEAT | UIM 2. | might get lost (downstream of altered splice site) | | 321 | 323 | REPEAT | 1. | might get lost (downstream of altered splice site) | | 321 | 406 | REGION | 5 X 3 AA repeats of [DE]-P-W. | might get lost (downstream of altered splice site) | | 344 | 346 | REPEAT | 2. | might get lost (downstream of altered splice site) | | 371 | 373 | REPEAT | 3. | might get lost (downstream of altered splice site) | | 375 | 375 | CONFLICT | R -> K (in Ref. 2; BAF85666). | might get lost (downstream of altered splice site) | | 387 | 389 | REPEAT | 4. | might get lost (downstream of altered splice site) | | 393 | 393 | MOD_RES | Phosphoserine (By similarity). | might get lost (downstream of altered splice site) | | 396 | 396 | CONFLICT | H -> Y (in Ref. 2; BAA91378). | might get lost (downstream of altered splice site) | | 404 | 406 | REPEAT | 5. | might get lost (downstream of altered splice site) | | 417 | 417 | CONFLICT | G -> S (in Ref. 2; BAF85666). | might get lost (downstream of altered splice site) | | 524 | 526 | REPEAT | 1. | might get lost (downstream of altered splice site) | | 524 | 631 | REGION | 3 X 3 AA repeats of N-P-F. | might get lost (downstream of altered splice site) | | 537 | 539 | REPEAT | 2. | might get lost (downstream of altered splice site) | | 629 | 631 | REPEAT | 3. | might get lost (downstream of altered splice site) |
|
| length of protein | N/A |
| AA sequence altered | N/A |
| position of stopcodon in wt / mu CDS | N/A |
| position (AA) of stopcodon in wt / mu AA sequence | N/A |
| position of stopcodon in wt / mu cDNA | N/A |
| 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 | 580 / 580 |
| chromosome | 17 |
| strand | 1 |
| last intron/exon boundary | 2165 |
| theoretical NMD boundary in CDS | 1535 |
| length of CDS | 1899 |
| coding sequence (CDS) position | N/A |
cDNA position
(for ins/del: last normal base / first normal base) | 369 |
gDNA position
(for ins/del: last normal base / first normal base) | 369 |
chromosomal position
(for ins/del: last normal base / first normal base) | 48610272 |
| original gDNA sequence snippet | TCCCGAGGCTGTGCCGTCCCGCTGCTGCACAGGTCGGAGGG |
| altered gDNA sequence snippet | TCCCGAGGCTGTGCCGTCCCCCTGCTGCACAGGTCGGAGGG |
| original cDNA sequence snippet | TCCCGAGGCTGTGCCGTCCCGCTGCTGCACAGGTCGGAGGG |
| altered cDNA sequence snippet | TCCCGAGGCTGTGCCGTCCCCCTGCTGCACAGGTCGGAGGG |
| wildtype AA sequence | MTTSALRRQV KNIVHNYSEA EIKVREATSN DPWGPPSSLM SEIADLTFNT VAFTEVMGML
WRRLNDSGKN WRHVYKALTL LDYLLKTGSE RVAHQCRENL YTIQTLKDFQ YIDRDGKDQG
VNVREKVKQV MALLKDEERL RQERTHALKT KERMALEGIG IGSGQLGFSR RYGEDYSRSR
GSPSSYNSSS SSPRYTSDLE QARPQTSGEE ELQLQLALAM SREEAEKPVP PASHRDEDLQ
LQLALRLSRQ EHEKEVRSWQ GDGSPMANGA GAVVHHQRDR EPEREERKEE EKLKTSQSSI
LDLADIFVPA LAPPSTHCSA DPWDIPGFRP NTEASGSSWG PSADPWSPIP SGTVLSRSQP
WDLTPMLSSS EPWGRTPVLP AGPPTTDPWA LNSPHHKLPS TGADPWGASL ETSDTPGGAS
TFDPFAKPPE STETKEGLEQ ALPSGKPSSP VELDLFGDPS PSSKQNGTKE PDALDLGILG
EALTQPSKEA RACRTPESFL GPSASSLVNL DSLVKAPQVA KTRNPFLTGL SAPSPTNPFG
AGEPGRPTLN QMRTGSPALG LAGGPVGAPL GSMTYSASLP LPLSSVPAGL TLPASVSVFP
QAGAFAPQPL LPTPSSAGPR PPPPQTGTNP FL* |
| mutated AA sequence | N/A |
| speed | 0.20 s |
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