Is HPS3 p.Ile807= (c.2421C>T) pathogenic?

HPS3 p.Ile807= (c.2421C>T) is classified Likely benign in HPS3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-02). Absent from gnomAD v4.1.

How common is HPS3 p.Ile807= (c.2421C>T) in the general population?

HPS3 p.Ile807= (c.2421C>T) is absent from gnomAD v4.1 (gnomAD).

HPS3 p.Ile807=

c.2421C>T · rs2473124417 · VCV2839843

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	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.1	GERP 0.2, phastCons 1
Overall
CADD	9.326	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.Ile807=
Coding: c.2421C>T
MANE Select: NM_000096 · reported on NM_032383
dbSNP: rs2473124417
Type: single nucleotide variant
Location: chr3:149162818 (GRCh38)

Full HPS3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-ile807 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown