Prediction |
polymorphism |
Model: without_aae, prob: 1.34346673037784e-24 (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) | chr14:21991626C>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | SALL2 |
| Ensembl transcript ID | ENST00000538754 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q9Y467 |
| alteration type | single base exchange |
| alteration region | intron |
| DNA changes | g.13725G>C |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs1263810
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 190 | 843 | 1033 |
| ExAC | 6080 | 20607 | 26687 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 1.717 | 0.941 | | 3.36 | 0.964 | | (flanking) | -0.366 | 0.06 |
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 | 13723 | wt: 0.44 / mu: 0.73 | wt: CGGGGCAGGGAGTTT
mu: CGGGGCACGGAGTTT | GGGC|aggg | | Donor increased | 13720 | wt: 0.73 / mu: 0.97 | wt: CTCCGGGGCAGGGAG
mu: CTCCGGGGCACGGAG | CCGG|ggca |
|
| distance from splice site | 1248 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 135 | 139 | COMPBIAS | Poly-Gly. | might get lost (downstream of altered splice site) | | 158 | 170 | COMPBIAS | Poly-Pro. | might get lost (downstream of altered splice site) | | 256 | 265 | COMPBIAS | Poly-Ser. | might get lost (downstream of altered splice site) | | 373 | 395 | ZN_FING | C2H2-type 1. | might get lost (downstream of altered splice site) | | 401 | 423 | ZN_FING | C2H2-type 2. | might get lost (downstream of altered splice site) | | 547 | 547 | CONFLICT | R -> L (in Ref. 1; X98834 and 5; AAI36529/AAI36530). | might get lost (downstream of altered splice site) | | 554 | 554 | CONFLICT | V -> M (in Ref. 1; X98834). | might get lost (downstream of altered splice site) | | 575 | 581 | CONFLICT | FPYVLEP -> LPLCARA (in Ref. 1; X98834). | might get lost (downstream of altered splice site) | | 609 | 609 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 616 | 616 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 623 | 623 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 631 | 653 | ZN_FING | C2H2-type 3. | might get lost (downstream of altered splice site) | | 659 | 681 | ZN_FING | C2H2-type 4. | might get lost (downstream of altered splice site) | | 691 | 713 | ZN_FING | C2H2-type 5. | might get lost (downstream of altered splice site) | | 764 | 775 | COMPBIAS | Poly-Glu. | might get lost (downstream of altered splice site) | | 797 | 797 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 802 | 802 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 806 | 806 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 816 | 821 | COMPBIAS | Poly-Ala. | might get lost (downstream of altered splice site) | | 838 | 843 | COMPBIAS | Poly-Pro. | might get lost (downstream of altered splice site) | | 911 | 911 | CROSSLNK | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin). | might get lost (downstream of altered splice site) | | 911 | 933 | ZN_FING | C2H2-type 6. | might get lost (downstream of altered splice site) | | 940 | 964 | ZN_FING | C2H2-type 7. | 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 | 374 / 374 |
| chromosome | 14 |
| strand | -1 |
| last intron/exon boundary | 759 |
| theoretical NMD boundary in CDS | 335 |
| length of CDS | 597 |
| coding sequence (CDS) position | N/A |
cDNA position
(for ins/del: last normal base / first normal base) | N/A |
gDNA position
(for ins/del: last normal base / first normal base) | 13725 |
chromosomal position
(for ins/del: last normal base / first normal base) | 21991626 |
| original gDNA sequence snippet | AATCTACAGTCTCCGGGGCAGGGAGTTTCCCCCAGCAGCAG |
| altered gDNA sequence snippet | AATCTACAGTCTCCGGGGCACGGAGTTTCCCCCAGCAGCAG |
| original cDNA sequence snippet | N/A |
| altered cDNA sequence snippet | N/A |
| wildtype AA sequence | MAHESERSSR LGVPCGEPAE LGGDASEEDH PQVCAKCCAQ FTDPTEFLAH QNACSTDPPV
MVIIGGQENP NNSSASSEPR PEGHNNPQVM DTEHSNPPDS GSSVPTDPTW GPERRGEESP
GHFLVAATEP VCGIPVKWPA HEALEFQLHL HYHSKPGPTS AVWPRNCGWE GASNNGIQGS
QGEDSPPPIS ASCTQGSA* |
| mutated AA sequence | N/A |
| speed | 0.77 s |
|
|
