# NM_003664.5(AP3B1):c.2478A>G (p.Pro826=)

https://sugi.bio/variant/ap3b1-p-pro826

## Summary

**AP3B1 p.Pro826= (c.2478A>G)** is classified **Likely benign** in AP3B1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-04). Very rare (popmax 0.00281%, nfe); Associated with Hermansky-Pudlak syndrome 2.

**At a glance:** Likely benign · review: Single submitter · rsID rs774139776 · 1 submitter · 1 linked condition · very rare (popmax 0.00281%, nfe)

## For patients & families {#patients}

This is a change in the AP3B1 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to Hermansky-Pudlak syndrome 2.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Adolescent, Infancy |
| Prevalence | 1-9 / 100 000 (Sweden) |
| Diagnostic panels | AP3B1 is a diagnostic-grade gene on 13 Genomics England panels |

**Commonly reported features of Familial hemophagocytic lymphohistiocytosis** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Thrombocytopenia — Very frequent (99-80%)
- Anemia — Very frequent (99-80%)
- Fever — Very frequent (99-80%)
- Elevated circulating hepatic transaminase concentration — Very frequent (99-80%)
- Immune dysregulation — Very frequent (99-80%)
- Hypoalbuminemia — Very frequent (99-80%)
- Increased circulating ferritin concentration — Very frequent (99-80%)
- Abnormality of serum cytokine level — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0015026/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [AP3B1](https://sugi.bio/atlas/gene/AP3B1/) |
| Protein change (HGVS p.) | p.Pro826= |
| Coding change (HGVS c.) | c.2478A>G |
| MANE Select transcript | [NM_003664](https://www.ncbi.nlm.nih.gov/nuccore/NM_003664) |
| dbSNP | [rs774139776](https://www.ncbi.nlm.nih.gov/snp/rs774139776/) |
| Variant type | single nucleotide variant |
| Location | chr5:78089492-78089492 (GRCh38) |
| ClinVar | [VCV2151325](https://www.ncbi.nlm.nih.gov/clinvar/variation/2151325/) |

**All HGVS expressions:** `LRG_170:g.210213A>G`, `LRG_170t1:c.2478A>G`, `NC_000005.10:g.78089492T>C`, `NC_000005.9:g.77385316T>C`, `NG_007268.1:g.210213A>G`, `NM_001271769.2:c.2331A>G`, `NM_001410752.1:c.2478A>G`, `NM_003664.5:c.2478A>G`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP -1.289, GERP -3.31 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 2.947**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00281%** (nfe) · FAF95 0.002% · FAF99 0.00176% · 33/1,175,646 in the highest group · 34/1,609,124 alleles overall — very rare (popmax 0.00281%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 0.00281% | 35,626 |
| African / African-American | 0.00134% | 74,816 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**AP3B1** population constraint: LOEUF 0.59, pLI 0.0032623, missense-Z 2.0333. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **Hermansky-Pudlak syndrome 2** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 75.85, 50% of residues very-high.

**5 experimental structure(s)** (PDB): [9C58](https://www.rcsb.org/structure/9C58), [9C59](https://www.rcsb.org/structure/9C59), [9C5A](https://www.rcsb.org/structure/9C5A), [9C5B](https://www.rcsb.org/structure/9C5B), [9C5C](https://www.rcsb.org/structure/9C5C).

## What this gene does {#gene-function}

*Describes the biological roles of AP3B1 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** AP3B1's established molecular role includes protein phosphatase binding. In Reactome, AP3B1 is annotated in disease pathway(s) including **Signaling by BRAF and RAF1 fusions**.

**Disease mechanism (Reactome):** AP3B1 loss or alteration is curated in [Signaling by BRAF and RAF1 fusions](https://reactome.org/content/detail/R-HSA-6802952).

### Pathways affected {#pathways}

AP3B1 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Signaling by BRAF and RAF1 fusions](https://reactome.org/content/detail/R-HSA-6802952) | curated |
| [Golgi Associated Vesicle Biogenesis](https://reactome.org/content/detail/R-HSA-432722) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** protein phosphatase binding, GTP-dependent protein binding.

**Biological process:** melanosome organization.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-05-04.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2025-05-04 |

## Associated conditions {#conditions}

[Hermansky-Pudlak syndrome 2](https://sugi.bio/atlas/disease/hermansky-pudlak-syndrome-2/).

**Reported phenotype names (ClinVar):** Hermansky-Pudlak syndrome 2, Platelet defects and oculocutaneous albinism.

## Similar variants {#similar}

Related AP3B1 variant pages (same residue, condition, or type): [AP3B1 c.2078-1G>A](/variant/ap3b1-c-2078-minus-1g-a), [AP3B1 c.280-2A>G](/variant/ap3b1-c-280-minus-2a-g), [AP3B1 p.Arg104Ter](/variant/ap3b1-p-arg104ter), [AP3B1 p.Arg649Ter](/variant/ap3b1-p-arg649ter), [AP3B1 c.128+4A>G](/variant/ap3b1-c-128-plus-4a-g), [AP3B1 c.2077+6T>C](/variant/ap3b1-c-2077-plus-6t-c), [AP3B1 c.2809+4A>G](/variant/ap3b1-c-2809-plus-4a-g), [AP3B1 c.2992+3G>A](/variant/ap3b1-c-2992-plus-3g-a).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 2151325). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*