| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000303142(MANE Select) | SHLD1 | Benign | 0|200 | without_ | No | Single base exchange | N/A |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr20:5834428A>G (GRCh38) | |||||||||||||
| Gene symbol | SHLD1 | |||||||||||||
| Gene constraints | LOEUF: 1.08, LOF (oe): 0.42, misssense (oe): 0.83, synonymous (oe): 0.94 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000303142.11 | |||||||||||||
| Genbank transcript ID | NM_152504 (exact from MANE), NM_001303477 (by similarity), NM_001303478 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.179-28596A>G g.84036A>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 | 20 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CAAACTCATCCAGCTGGGTTACATTCTAATTTGACCAATGA | |||||||||||||
| Altered gDNA sequence snippet | CAAACTCATCCAGCTGGGTTGCATTCTAATTTGACCAATGA | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MAARDATSGS LSEESSALDL PSACDIRDYV LQGPSQEANS EAFSSLEFHS FPYSSDVDPD TSNLNIEQNN SWTAENFWLD PAVKGQSEKE EDDGLRKSLD RFYEMFGHPQ PGSANSLSAS VCKCLSQKIT QLRGQESQKY ALRSFQMARV IFNRDGCSVL QRHSRDTHFY PLEEGSTSLD DEKPNPGLSK DITHFLLQQN VMKDL* | |||||||||||||
| 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 | 84 / 84 | |||||||||||||
| Last intron/exon boundary | 261 | |||||||||||||
| Theoretical NMD boundary in CDS | 127 | |||||||||||||
| Length of CDS | 618 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 84036 | |||||||||||||
| Chromosomal position | 5834428 | |||||||||||||
| 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