Is HPS3 p.Glu930fs (c.2788_2792del) pathogenic?

HPS3 p.Glu930fs (c.27882792del) is classified Likely pathogenic in HPS3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-15). No gnomAD frequency available for this variant; Associated with Hermansky-Pudlak syndrome.

What condition is associated with HPS3 p.Glu930fs (c.2788_2792del)?

HPS3 p.Glu930fs (c.2788_2792del) is associated with Hermansky-Pudlak syndrome (ClinVar).

How common is HPS3 p.Glu930fs (c.2788_2792del) in the general population?

HPS3 p.Glu930fs (c.2788_2792del) is no gnomAD frequency available for this variant (gnomAD).

How is Hermansky-Pudlak syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

HPS3 p.Glu930fs

c.2788_2792del · rs2472689274 · VCV2501269

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Hermansky-Pudlak syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.4	GERP 2.1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

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: HPS3
Protein: p.Glu930fs
Coding: c.2788_2792del
MANE Select: NM_000096 · reported on NM_032383
dbSNP: rs2472689274
Type: Deletion
Location: chr3:149167228 (GRCh38)

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

Disease context

Hermansky-Pudlak syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hermansky-Pudlak syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Worldwide)

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-glu930fs (accessed [today's date]).

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