| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000356692(MANE Select) | PPP4R2 | Benign | 0|200 | without_ | No | Single base exchange | N/A |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:73053574A>G (GRCh38) | |||||||||||||
| Gene symbol | PPP4R2 | |||||||||||||
| Gene constraints | LOEUF: 0.81, LOF (oe): 0.49, misssense (oe): 1.08, synonymous (oe): 1.05 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000356692.10 | |||||||||||||
| Genbank transcript ID | NM_174907 (exact from MANE), NM_001318026 (by similarity), NM_001318025 (by similarity), NM_001318027 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.288-5463A>G g.56772A>G | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| 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? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | GGTCAAGGAGTGGTGCAGACATTAGTTTACTTACATCATTG | |||||||||||||
| Altered gDNA sequence snippet | GGTCAAGGAGTGGTGCAGACGTTAGTTTACTTACATCATTG | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MDVERLQEAL KDFEKRGKKE VCPVLDQFLC HVAKTGETMI QWSQFKGYFI FKLEKVMDDF RTSAPEPRGP PNPNVEYIPF DEMKERILKI VTGFNGIPFT IQRLCELLTD PRRNYTGTDK FLRGVEKNVM VVSCVYPSSE KNNSNSLNRM NGVMFPGNSP SYTERSNING PGTPRPLNRP KVSLSAPMTT NGLPESTDSK EANLQQNEEK NHSDSSTSES EVSSVSPLKN KHPDEDAVEA EGHEVKRLRF DKEGEVRETA SQTTSSEISS VMVGETEASS SSQDKDKDSR CTRQHCTEED EEEDEEEEEE SFMTSREMIP ERKNQEKESD DALTVNEETS EENNQMEESD VSQAEKDLLH SEGSENEGPV SSSSSDCRET EELVGSNSSK TGEILSESSM ENDDEATEVT DEPMEQD* | |||||||||||||
| Mutated AA sequence | ||||||||||||||
| 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 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 228 / 228 | |||||||||||||
| Last intron/exon boundary | 1155 | |||||||||||||
| Theoretical NMD boundary in CDS | 877 | |||||||||||||
| Length of CDS | 1254 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 56772 | |||||||||||||
| Chromosomal position | 73053574 | |||||||||||||
| 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