| Transcript | Gene symbol | Prediction | Tree vote | Model | Prediction problem | Splice site change | Known ClinVar disease mutation | Potential ClinVar disease mutation | Amino acid changes | Variant type | dbSNP ID | Protein length | Features at a glance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000290541(MANE Select) | PSMB4 | Benign | 2|198 | without_ | No | Single base exchange | Normal |
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr1:151399626G>T (GRCh38) | |||||||||||||
| Gene symbol | PSMB4 | |||||||||||||
| Gene constraints | LOEUF: 0.66, LOF (oe): 0.43, misssense (oe): 0.89, synonymous (oe): 1.00 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000290541.7 | |||||||||||||
| Genbank transcript ID | NM_002796 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.39G>T g.67G>T | |||||||||||||
| AA changes | no AA changes | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | No | |||||||||||||
| Chromosome | 1 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TCGCGGTCCGGACTTTGGGCGGGGGGTCCGGCCCCAGGACA | |||||||||||||
| Altered gDNA sequence snippet | TCGCGGTCCGGACTTTGGGCTGGGGGTCCGGCCCCAGGACA | |||||||||||||
| Original cDNA sequence snippet | TCGCGGTCCGGACTTTGGGCGGGGGGTCCGGCCCCAGGACA | |||||||||||||
| Altered cDNA sequence snippet | TCGCGGTCCGGACTTTGGGCTGGGGGTCCGGCCCCAGGACA | |||||||||||||
| Wildtype AA sequence | MEAFLGSRSG LWAGGPAPGQ FYRIPSTPDS FMDPASALYR GPITRTQNPM VTGTSVLGVK FEGGVVIAAD MLGSYGSLAR FRNISRIMRV NNSTMLGASG DYADFQYLKQ VLGQMVIDEE LLGDGHSYSP RAIHSWLTRA MYSRRSKMNP LWNTMVIGGY ADGESFLGYV DMLGVAYEAP SLATGYGAYL AQPLLREVLE KQPVLSQTEA RDLVERCMRV LYYRDARSYN RFQIATVTEK GVEIEGPLST ETNWDIAHMI SGFE* | |||||||||||||
| Mutated AA sequence | MEAFLGSRSG LWAGGPAPGQ FYRIPSTPDS FMDPASALYR GPITRTQNPM VTGTSVLGVK FEGGVVIAAD MLGSYGSLAR FRNISRIMRV NNSTMLGASG DYADFQYLKQ VLGQMVIDEE LLGDGHSYSP RAIHSWLTRA MYSRRSKMNP LWNTMVIGGY ADGESFLGYV DMLGVAYEAP SLATGYGAYL AQPLLREVLE KQPVLSQTEA RDLVERCMRV LYYRDARSYN RFQIATVTEK GVEIEGPLST ETNWDIAHMI SGFE* | |||||||||||||
| 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 | 810 / 810 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 16 / 16 | |||||||||||||
| Last intron/exon boundary | 797 | |||||||||||||
| Theoretical NMD boundary in CDS | 731 | |||||||||||||
| Length of CDS | 795 | |||||||||||||
| Coding sequence (CDS) position | 39 | |||||||||||||
| cDNA position | 54 | |||||||||||||
| gDNA position | 67 | |||||||||||||
| Chromosomal position | 151399626 | |||||||||||||
| Speed | 0.02 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project