Table II.
Genetic characterization of the PMVK variant
| Gene description | |
|---|---|
| HGNC_ID | HGNC:9141 |
| CCDS SIZE (INCLUDING UTRS) (NM_006556.4) | 1002 |
| EXONS, N | 5 |
| LOEUF SCORE (GNOMAD V2.1.1) | 1.395 |
| UNIQUE PROTEIN-CODING VARIANTS (GNOMAD V2.1.1), N | 97 missense, 8 pLoF |
| Variant description | |
|---|---|
| Genome Reference Consortium Human Build | B38 |
| CHROMOSOME | Chr1 |
| POSITION | 154926404 |
| NT_REF | A |
| NT_ALT | G |
| CDNA_CHANGE | NM_006556.4: c.392T>C |
| AA_CHANGE | p.Val131Ala |
| Gnomad_Af (Gnomad V3.1.2) | NA |
| In silico pathogenicity assessment | |
|---|---|
| PolyPhen2_HVAR_score (PolyPhen-2 v2.2.2) | 0,992 |
| PolyPhen_prediction | Probably damaging |
| SIFT_score (SIFT ENSEMBL 66) | 0 |
| SIFT_prediction | Deleterious |
| CADD_v1.6 | 23.5 |
| REVEL (release May 3, 2021) | 0.389 |
| MutationTaster2 (update 2015) | 0.999983 |
| PROVEAN_score (version 1.1 ENSEMBL 66) | −3.86 |
AA, Aminoacid; AF, allel frequency; ALT, alternative allele; CCDS, Consensus coding sequence; HGNC_ID, HUGO Gene Nomenclature Committee identifier; HVAR, HumVar training set; LOEUF, Loss-of-function observed/expected upper bound fraction; NA, not available; pLoF, putative loss of function; REF, reference allele.