# NM_001272071.2(AP1S2):c.386A>C (p.Asn129Thr)

https://sugi.bio/variant/ap1s2-p-asn129thr

## Summary

**AP1S2 p.Asn129Thr (c.386A>C)** is classified **Uncertain significance** in AP1S2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-09). AlphaMissense: likely benign (0.0615); Absent from gnomAD v4.1.

**At a glance:** Uncertain significance · review: Multiple submitters · 2 submitters · AlphaMissense likely benign · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the AP1S2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters.

*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.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [AP1S2](https://sugi.bio/atlas/gene/AP1S2/) |
| Protein change (HGVS p.) | p.Asn129Thr |
| Coding change (HGVS c.) | c.386A>C |
| MANE Select transcript | [NM_001272071](https://www.ncbi.nlm.nih.gov/nuccore/NM_001272071) |
| Variant type | single nucleotide variant |
| Location | chrX:15845419-15845419 (GRCh38) |
| ClinVar | [VCV3620205](https://www.ncbi.nlm.nih.gov/clinvar/variation/3620205/) |

**All HGVS expressions:** `NC_000023.10:g.15863542T>G`, `NC_000023.11:g.15845419T>G`, `NG_009274.2:g.14559A>C`, `NM_001272071.2:c.386A>C`, `NM_001368994.1:c.386A>C`, `NM_001369007.1:c.386A>C`, `NM_001369008.1:c.386A>C`, `NM_003916.3:c.386A>C`, `NM_003916.5:c.386A>C`, `NR_160932.1:n.512A>C`, `NR_160933.1:n.512A>C`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.0615)
- REVEL 0.38 (indeterminate)
- SaProt LLR -10.499 (damaging) — differs from AlphaMissense
- → **In-silico consensus:** SaProt calls this damaging; AlphaMissense does not; REVEL makes no call
- Conservation: phyloP 7.845, GERP 1.89, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 23.7**. 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.*
- Regional missense constraint: **o/e 0.58** across the covering region of the MANE Select transcript (15,827,328–15,845,419), spanning 18,091 bp. Chi-square p 0.042. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code 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: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**AP1S2** population constraint: ClinGen dosage — haploinsufficiency 3, triplosensitivity 0 (0–3 scale). *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):

- **X-linked syndromic complex neurodevelopmental disorder** — Definitive (XL)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 94.36, 91% of residues very-high.

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

*Describes the biological roles of AP1S2 (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:** AP1S2 participates in disease-associated pathways. In Reactome, AP1S2 is annotated in disease pathway(s) including **Nef mediated downregulation of MHC class I complex cell surface expression**.

**Disease mechanism (Reactome):** AP1S2 loss or alteration is curated in [Nef mediated downregulation of MHC class I complex cell surface expression](https://reactome.org/content/detail/R-HSA-164940).

### Pathways affected {#pathways}

AP1S2 participates in **4 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Nef mediated downregulation of MHC class I complex cell surface expression](https://reactome.org/content/detail/R-HSA-164940) | curated |
| [Golgi Associated Vesicle Biogenesis](https://reactome.org/content/detail/R-HSA-432722) | curated |
| [Lysosome Vesicle Biogenesis](https://reactome.org/content/detail/R-HSA-432720) | curated |
| [MHC class II antigen presentation](https://reactome.org/content/detail/R-HSA-2132295) | curated |

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2024-10-09.

**Submitter consensus:** unanimous (2/2 Uncertain significance).

**Submission history:** 2 submissions (2024); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-06-23 |
| GeneDx | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-10-09 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Similar variants {#similar}

Related AP1S2 variant pages (same residue, condition, or type): [AP1S2 p.Asn129Ile](/variant/ap1s2-p-asn129ile), [AP1S2 c.-1+1G>A](/variant/ap1s2-c-minus-1-plus-1g-a), [AP1S2 p.Arg52Ter](/variant/ap1s2-p-arg52ter), [AP1S2 p.Gln123Ter](/variant/ap1s2-p-gln123ter), [AP1S2 p.Gly158Arg](/variant/ap1s2-p-gly158arg), [AP1S2 p.Ile134Thr](/variant/ap1s2-p-ile134thr), [AP1S2 p.Ile82Val](/variant/ap1s2-p-ile82val), [AP1S2 p.Leu54Val](/variant/ap1s2-p-leu54val).

### 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 3620205). 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.*