HPS5 p.Phe656=
c.1968T>C · rs2494604456 · VCV2770229
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 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.01 | GERP -5.1 |
| Overall | ||
| CADD | 3.216 | 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
- HPS5
- Protein
- p.Phe656=
- Coding
- c.1968T>C
- MANE Select
- NM_181507
- dbSNP
- rs2494604456
- Type
- single nucleotide variant
- Location
- chr11:18291914 (GRCh38)
- Gene constraint
- LOEUF 0.797 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.21
Similar variants
- HPS5 p.Phe656Ser Uncertain significance ★★ ⚠ same residue
- HPS5 c.1164+1G>A Likely pathogenic ★★ same type
- HPS5 c.1862+1G>A Likely pathogenic ★★ same type
- HPS5 c.220-1G>T Pathogenic ★★ same type
- HPS5 c.2718-2A>G Pathogenic/Likely pathogenic ★★ same type
- HPS5 c.2837+1G>A Likely pathogenic ★★ same type
- HPS5 c.2952-1G>C Likely pathogenic ★★ same type
- HPS5 c.478-2A>G 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/hps5-p-phe656 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown