PCNT p.Ser485fs
c.1454del · rs2518099852 · VCV2710300
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 9 of 47 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP -2.2, phastCons 0.009 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PCNT
- Protein
- p.Ser485fs
- Coding
- c.1454del
- MANE Select
- NM_006031
- dbSNP
- rs2518099852
- Type
- Deletion
- Location
- chr21:46351538 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
Similar variants
- PCNT c.2155-21_2186del Likely pathogenic ★★ same type
- PCNT p.Ala995fs Pathogenic ★★ same type
- PCNT p.Glu3290fs Pathogenic/Likely pathogenic ★★ same type
- PCNT p.Gly1667fs Pathogenic/Likely pathogenic ★★ same type
- PCNT p.His203fs Pathogenic/Likely pathogenic ★★ same type
- PCNT p.Leu1091fs Pathogenic/Likely pathogenic ★★ same type
- PCNT p.Leu1910fs Pathogenic/Likely pathogenic ★★ same type
- PCNT p.Phe133fs Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/pcnt-p-ser485fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown