| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000220812(MANE Select) | DKK4 | Deleterious | 90|10 | simple_ | No | Single base exchange | Normal |
|
| Analysed issue | Analysis result | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr8:42374123A>C (GRCh38) | |||||||||||||||||||||
| Gene symbol | DKK4 | |||||||||||||||||||||
| Gene constraints | LOEUF: 1.64, LOF (oe): 1.13, misssense (oe): 0.93, synonymous (oe): 0.80 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000220812.3 | |||||||||||||||||||||
| Genbank transcript ID | NM_014420 (exact from MANE) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | DKK4_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.652T>G g.3107T>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| 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 | Yes | |||||||||||||||||||||
| Chromosome | 8 | |||||||||||||||||||||
| Strand | -1 | |||||||||||||||||||||
| Original gDNA sequence snippet | AGCATGCTCGATTAAGAGTATGCCAAAAAATAGAAAAGCTA | |||||||||||||||||||||
| Altered gDNA sequence snippet | AGCATGCTCGATTAAGAGTAGGCCAAAAAATAGAAAAGCTA | |||||||||||||||||||||
| Original cDNA sequence snippet | AGCATGCTCGATTAAGAGTATGCCAAAAAATAGAAAAGCTA | |||||||||||||||||||||
| Altered cDNA sequence snippet | AGCATGCTCGATTAAGAGTAGGCCAAAAAATAGAAAAGCTA | |||||||||||||||||||||
| Wildtype AA sequence | MVAAVLLGLS WLCSPLGALV LDFNNIRSSA DLHGARKGSQ CLSDTDCNTR KFCLQPRDEK PFCATCRGLR RRCQRDAMCC PGTLCVNDVC TTMEDATPIL ERQLDEQDGT HAEGTTGHPV QENQPKRKPS IKKSQGRKGQ EGESCLRTFD CGPGLCCARH FWTKICKPVL LEGQVCSRRG HKDTAQAPEI FQRCDCGPGL LCRSQLTSNR QHARLRVCQK IEKL* | |||||||||||||||||||||
| Mutated AA sequence | MVAAVLLGLS WLCSPLGALV LDFNNIRSSA DLHGARKGSQ CLSDTDCNTR KFCLQPRDEK PFCATCRGLR RRCQRDAMCC PGTLCVNDVC TTMEDATPIL ERQLDEQDGT HAEGTTGHPV QENQPKRKPS IKKSQGRKGQ EGESCLRTFD CGPGLCCARH FWTKICKPVL LEGQVCSRRG HKDTAQAPEI FQRCDCGPGL LCRSQLTSNR QHARLRVGQK IEKL* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 675 / 675 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 225 / 225 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 859 / 859 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 185 / 185 | |||||||||||||||||||||
| Last intron/exon boundary | 599 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 364 | |||||||||||||||||||||
| Length of CDS | 675 | |||||||||||||||||||||
| Coding sequence (CDS) position | 652 | |||||||||||||||||||||
| cDNA position | 836 | |||||||||||||||||||||
| gDNA position | 3107 | |||||||||||||||||||||
| Chromosomal position | 42374123 | |||||||||||||||||||||
| Speed | 0.07 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