Prediction |
polymorphism |
Model: simple_aae, prob: 0.997289500529935 (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 CM094608)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr15:89450587G>TN/A
show variant in all transcripts IGV
|
| HGNC symbol | MFGE8 |
| Ensembl transcript ID | ENST00000542878 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q08431 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.94C>A
cDNA.154C>A
g.6056C>A |
| AA changes | L32M Score: 15 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 32 |
| frameshift | no |
| known variant | Reference ID: rs1878326
| database | homozygous (T/T) | heterozygous | allele carriers |
| 1000G | 1056 | 1085 | 2141 |
| ExAC | 23799 | -14831 | 8968 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM094608)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 4.77 | 1 | | 0.987 | 1 | | (flanking) | 1.489 | 1 |
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 | 6058 | wt: 0.4449 / mu: 0.4452 (marginal change - not scored) | wt: GGCCTGGAGAATGGG
mu: GGCATGGAGAATGGG | CCTG|gaga | | Donor increased | 6057 | wt: 0.30 / mu: 0.44 | wt: GGGCCTGGAGAATGG
mu: GGGCATGGAGAATGG | GCCT|ggag | | Donor gained | 6052 | 0.87 | mu: CCACTGGGCATGGAG | ACTG|ggca |
|
| distance from splice site | 21 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 32 | L | V | A | L | E | C | V | E | P | L | G | L | E | N | G | N | I | A | N | S | Q | I | A | A |
| mutated | all conserved | | 32 | L | V | A | L | E | C | V | E | P | L | G | M | E | N | G | N | I | A | N | S | Q | I | A |
| Ptroglodytes | all conserved | ENSPTRG00000007426 | 67 | | | | | YAGNHCETK | C | V | E | P | L | G | M | E | N | G | N | I | A | N | S | Q | I | A |
| Mmulatta | no homologue | | | |
| Fcatus | no homologue | | | |
| Mmusculus | all conserved | ENSMUSG00000030605 | 154 | | L | A | S | R | C | S | T | Q | L | G | M | E | G | G | A | I | A | D | S | Q | I | S |
| Ggallus | all conserved | ENSGALG00000006702 | 154 | | | | | | C | A | I | P | L | G | M | E | G | G | A | I | S | D | A | Q | L | S |
| Trubripes | all conserved | ENSTRUG00000016888 | 161 | | | | | | C | T | S | L | L | G | M | E | G | G | A | I | V | E | S | Q | I | S |
| Drerio | all conserved | ENSDARG00000045803 | 159 | | | | L | R | C | I | S | L | L | G | M | E | G | G | G | I | A | E | S | Q | I | S |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | all conserved | ENSXETG00000017772 | 157 | | | | I | R | C | A | N | A | L | G | M | E | G | R | A | I | S | D | A | Q | I | T |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 24 | 67 | DOMAIN | EGF-like. | lost | | 32 | 32 | DISULFID | By similarity. | lost | | 38 | 38 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 46 | 48 | MOTIF | Cell attachment site. | might get lost (downstream of altered splice site) | | 55 | 55 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 57 | 57 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 66 | 66 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 70 | 70 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 70 | 225 | DOMAIN | F5/8 type C 1. | might get lost (downstream of altered splice site) | | 212 | 212 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 216 | 216 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 225 | 225 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 228 | 228 | CARBOHYD | N-linked (GlcNAc...); atypical. | might get lost (downstream of altered splice site) | | 230 | 230 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 230 | 387 | DOMAIN | F5/8 type C 2. | might get lost (downstream of altered splice site) | | 238 | 238 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 268 | 268 | CONFLICT | R -> W (in Ref. 5; CAD97938). | might get lost (downstream of altered splice site) | | 325 | 325 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 329 | 329 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 350 | 350 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 352 | 352 | CONFLICT | S -> T (in Ref. 5; CAD97938). | might get lost (downstream of altered splice site) | | 387 | 387 | DISULFID | By similarity. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1032 / 1032 |
| position (AA) of stopcodon in wt / mu AA sequence | 344 / 344 |
| position of stopcodon in wt / mu cDNA | 1092 / 1092 |
| 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 | 61 / 61 |
| chromosome | 15 |
| strand | -1 |
| last intron/exon boundary | 955 |
| theoretical NMD boundary in CDS | 844 |
| length of CDS | 1032 |
| coding sequence (CDS) position | 94 |
cDNA position
(for ins/del: last normal base / first normal base) | 154 |
gDNA position
(for ins/del: last normal base / first normal base) | 6056 |
chromosomal position
(for ins/del: last normal base / first normal base) | 89450587 |
| original gDNA sequence snippet | AATGTGTCGAGCCACTGGGCCTGGAGAATGGGAACATTGCC |
| altered gDNA sequence snippet | AATGTGTCGAGCCACTGGGCATGGAGAATGGGAACATTGCC |
| original cDNA sequence snippet | AATGTGTCGAGCCACTGGGCCTGGAGAATGGGAACATTGCC |
| altered cDNA sequence snippet | AATGTGTCGAGCCACTGGGCATGGAGAATGGGAACATTGCC |
| wildtype AA sequence | MPRPRLLAAL CGALLCAPSL LVALECVEPL GLENGNIANS QIAASSVRVT FLGLQHWVPE
LARLNRAGMV NAWTPSSNDD NPWIQVNLLR RMWVTGVVTQ GASRLASHEY LKAFKVAYSL
NGHEFDFIHD VNKKHKEFVG NWNKNAVHVN LFETPVEAQY VRLYPTSCHT ACTLRFELLG
CELNGCANPL GLKNNSIPDK QITASSSYKT WGLHLFSWNP SYARLDKQGN FNAWVAGSYG
NDQWLQVDLG SSKEVTGIIT QGARNFGSVQ FVASYKVAYS NDSANWTEYQ DPRTGSSKIF
PGNWDNHSHK KNLFETPILA RYVRILPVAW HNRIALRLEL LGC* |
| mutated AA sequence | MPRPRLLAAL CGALLCAPSL LVALECVEPL GMENGNIANS QIAASSVRVT FLGLQHWVPE
LARLNRAGMV NAWTPSSNDD NPWIQVNLLR RMWVTGVVTQ GASRLASHEY LKAFKVAYSL
NGHEFDFIHD VNKKHKEFVG NWNKNAVHVN LFETPVEAQY VRLYPTSCHT ACTLRFELLG
CELNGCANPL GLKNNSIPDK QITASSSYKT WGLHLFSWNP SYARLDKQGN FNAWVAGSYG
NDQWLQVDLG SSKEVTGIIT QGARNFGSVQ FVASYKVAYS NDSANWTEYQ DPRTGSSKIF
PGNWDNHSHK KNLFETPILA RYVRILPVAW HNRIALRLEL LGC* |
| speed | 1.18 s |
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