# NM_005224.3(ARID3A):c.1729C>T (p.Pro577Ser)

https://sugi.bio/variant/arid3a-p-pro577ser

## Summary

**ARID3A p.Pro577Ser (c.1729C>T)** is classified **Uncertain significance** in ARID3A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-19). AlphaMissense: likely benign (0.0628); Very rare (popmax 0.00777%, sas).

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · AlphaMissense likely benign · very rare (popmax 0.00777%, sas)

## For patients & families {#patients}

This is a change in the ARID3A gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter.

*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 | [ARID3A](https://sugi.bio/atlas/gene/ARID3A/) |
| Protein change (HGVS p.) | p.Pro577Ser |
| Coding change (HGVS c.) | c.1729C>T |
| MANE Select transcript | [NM_005224](https://www.ncbi.nlm.nih.gov/nuccore/NM_005224) |
| Variant type | single nucleotide variant |
| Location | chr19:972012-972012 (GRCh38) |
| ClinVar | [VCV3784584](https://www.ncbi.nlm.nih.gov/clinvar/variation/3784584/) |

**All HGVS expressions:** `NC_000019.10:g.972012C>T`, `NC_000019.9:g.972012C>T`, `NM_005224.3:c.1729C>T`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.0628)
- REVEL 0.052 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -5.377 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- SpliceAI predicts **donor gain** (Δ 0.35) — a splice-altering prediction on an uncertain variant — a signal for review
- Conservation: phyloP 0.146, GERP -2.68, phastCons 0.028 — weakly conserved position
- CADD: **PHRED 10.29**. 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 0.87** across the covering region of the MANE Select transcript (964,927–972,062), spanning 7,135 bp. Chi-square p 0.013. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI deltas (raw): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.35**. Largest is donor gain.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.35**.
- Pangolin: Δ**0.37** (gain), gain 0.37 / loss 0.00. Agrees with SpliceAI. An independent predictor to SpliceAI — a different model trained on different data. *Descriptive; ClinGen's SVI calibration covers SpliceAI, not Pangolin, so no ACMG code is assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.00777%** (sas) · FAF95 0.00362% · FAF99 0.00257% · 7/90,136 in the highest group · 8/1,598,742 alleles overall — very rare (popmax 0.00777%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 0.00777% | 12,877 |
| Remaining individuals (not grpmax-eligible) | 0.00162% | 61,732 |

*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}

**ARID3A** population constraint: LOEUF 0.442, pLI 0.99829, missense-Z 0.66049. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **577** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 62.23, 22% of residues very-high.

**2 experimental structure(s)** (PDB): [2KK0](https://www.rcsb.org/structure/2KK0), [4LJX](https://www.rcsb.org/structure/4LJX).

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

*Describes the biological roles of ARID3A (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.*


### Pathways affected {#pathways}

ARID3A participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest](https://reactome.org/content/detail/R-HSA-6804116) | curated |

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-01-19.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-01-19 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related ARID3A variant pages (same residue, condition, or type): [ARID3A c.950+3G>A](/variant/arid3a-c-950-plus-3g-a), [ARID3A p.Ala486=](/variant/arid3a-p-ala486), [ARID3A p.Glu447=](/variant/arid3a-p-glu447), [ARID3A p.Gly551=](/variant/arid3a-p-gly551), [ARID3A p.Ser522=](/variant/arid3a-p-ser522), [ARID3A p.Ala171Thr](/variant/arid3a-p-ala171thr), [ARID3A p.Ala182Val](/variant/arid3a-p-ala182val), [ARID3A p.Ala209Thr](/variant/arid3a-p-ala209thr).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 2026-10-14); 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 3784584). 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.*