HPS3 p.Arg397=
c.1191G>C · rs1159935157 · VCV2061821
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.38 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 6.404 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
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.Arg397=
- Coding
- c.1191G>C
- MANE Select
- NM_032383
- dbSNP
- rs1159935157
- Type
- single nucleotide variant
- Location
- chr3:149150626 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.67
- Residue 397
- a UniProt-annotated variant site (in a colorectal cancer sample; somatic mutation); a UniProt-annotated variant site (in hps3; mild)
Similar variants
- HPS3 p.Arg397Trp Pathogenic/Likely pathogenic ★★ ⚠ same residue
- HPS3 c.1163+1G>A Pathogenic ★★ same type
- HPS3 c.1246-2A>T Likely pathogenic ★★ same type
- HPS3 c.1509+1G>A Likely pathogenic ★★ same type
- HPS3 c.1691+1G>A Pathogenic ★★ same type
- HPS3 c.1692-2A>G Likely pathogenic ★★ same type
- HPS3 c.1873-1G>A Likely pathogenic ★★ same type
- HPS3 c.2106+1G>T 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/hps3-p-arg397 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown