HPS3 p.Phe781Ser
c.2342T>C · rs2108170322 · VCV1463689
⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why
Computational evidence
| Protein change | ||
| AlphaMissense | 0.5391 | ambiguous |
|---|---|---|
| REVEL | 0.746 | pathogenic-leaning |
| SaProt | LLR -7.90 | tolerated |
| ⇒ REVEL calls this damaging; SaProt does not; AlphaMissense is indeterminate. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.99 | unconstrained · MANE · 42 kb · p 0.79 · regional, not allelic |
| Overall | ||
| CADD | 27.4 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- HPS3
- Protein
- p.Phe781Ser
- Coding
- c.2342T>C
- MANE Select
- NM_032383
- dbSNP
- rs2108170322
- Type
- single nucleotide variant
- Location
- chr3:149162739 (GRCh38)
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/hps3-p-phe781ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown