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
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hyperlink |
analysed issue |
analysis result |
name of alteration | no title |
alteration (phys. location) | chr14:21991626C>GN/A
show variant in all transcripts IGV
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HGNC symbol | SALL2 |
Ensembl transcript ID | ENST00000317492 |
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 |
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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 | 13720 | wt: 0.73 / mu: 0.97 | wt: CTCCGGGGCAGGGAG mu: CTCCGGGGCACGGAG | CCGG|ggca | Donor increased | 13723 | wt: 0.44 / mu: 0.73 | wt: CGGGGCAGGGAGTTT mu: CGGGGCACGGAGTTT | GGGC|aggg |
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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) |
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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 | 14 / 14 |
chromosome | 14 |
strand | -1 |
last intron/exon boundary | 405 |
theoretical NMD boundary in CDS | 341 |
length of CDS | 603 |
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 | MSRRKQRKPQ QLISDCEGPS ASENGDASEE DHPQVCAKCC AQFTDPTEFL AHQNACSTDP PVMVIIGGQE NPNNSSASSE PRPEGHNNPQ VMDTEHSNPP DSGSSVPTDP TWGPERRGEE SPGHFLVAAT EPVCGIPVKW PAHEALEFQL HLHYHSKPGP TSAVWPRNCG WEGASNNGIQ GSQGEDSPPP ISASCTQGSA * |
mutated AA sequence | N/A |
speed | 0.82 s |
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