# NM_152641.4(ARID2):c.1673G>C (p.Arg558Pro)

https://sugi.bio/variant/arid2-p-arg558pro

## Summary

**ARID2 p.Arg558Pro (c.1673G>C)** is classified **Uncertain significance** in ARID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-08-05). AlphaMissense: likely pathogenic (0.9921); Absent from gnomAD v4.1.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs1331723696 · 1 submitter · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the ARID2 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 | [ARID2](https://sugi.bio/atlas/gene/ARID2/) |
| Protein change (HGVS p.) | p.Arg558Pro |
| Coding change (HGVS c.) | c.1673G>C |
| MANE Select transcript | [NM_152641](https://www.ncbi.nlm.nih.gov/nuccore/NM_152641) |
| dbSNP | [rs1331723696](https://www.ncbi.nlm.nih.gov/snp/rs1331723696/) |
| Variant type | single nucleotide variant |
| Location | chr12:45848928-45848928 (GRCh38) |
| ClinVar | [VCV1302414](https://www.ncbi.nlm.nih.gov/clinvar/variation/1302414/) |

**All HGVS expressions:** `NC_000012.11:g.46242711G>C`, `NC_000012.12:g.45848928G>C`, `NG_052800.1:g.124264G>C`, `NM_001347839.2:c.1673G>C`, `NM_152641.4:c.1673G>C`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.9921)
- REVEL 0.79 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -6.095 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense and REVEL call this damaging; SaProt does not
- Conservation: phyloP 11.805, GERP 2.62, phastCons 1 — highly conserved (agrees)
- AlphaMissense ranks this among the **top 7%** most-pathogenic-predicted substitutions in ARID2 (of 10,704 modeled).
- CADD: **PHRED 29.0**. 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 0.86** across the covering region of the MANE Select transcript (45,839,399–45,851,600), spanning 12,201 bp. Chi-square p 0.0001. 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}

**ARID2** population constraint: LOEUF 0.224, pLI 1, missense-Z 4.4902; 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):

- **Coffin-Siris syndrome** — Definitive (AD)

## Protein context {#protein}

Residue **558** lies in a DNA-binding region; a UniProt-annotated variant site (in css6).

AlphaFold model confidence (whole protein): pLDDT 52.30, 16% of residues very-high.

**2 experimental structure(s)** (PDB): [7VDV](https://www.rcsb.org/structure/7VDV), [7Y8R](https://www.rcsb.org/structure/7Y8R).

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

*Describes the biological roles of ARID2 (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:** ARID2's established molecular role includes DNA binding. p.Arg558Pro falls in a DNA-binding region.


### Pathways affected {#pathways}

ARID2 participates in **4 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Formation of the polybromo-BAF (pBAF) complex](https://reactome.org/content/detail/R-HSA-9933939) | curated |
| [RMTs methylate histone arginines](https://reactome.org/content/detail/R-HSA-3214858) | curated |
| [RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known](https://reactome.org/content/detail/R-HSA-8939243) | curated |
| [SWI/SNF chromatin remodelers](https://reactome.org/content/detail/R-HSA-9932451) | curated |

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

**Molecular function:** DNA binding.

**Biological process:** nucleosome disassembly, negative regulation of cell population proliferation, negative regulation of cell migration, positive regulation of double-strand break repair via homologous recombination.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2020-08-05.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Uncertain significance | criteria provided, single submitter | clinical testing | 2020-08-05 |

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

## Similar variants {#similar}

Related ARID2 variant pages (same residue, condition, or type): [ARID2 p.Arg558His](/variant/arid2-p-arg558his), [ARID2 p.Arg1272Ter](/variant/arid2-p-arg1272ter), [ARID2 p.Arg1677Ter](/variant/arid2-p-arg1677ter), [ARID2 p.Arg1754Ter](/variant/arid2-p-arg1754ter), [ARID2 p.Arg1769Ter](/variant/arid2-p-arg1769ter), [ARID2 p.Arg274Ter](/variant/arid2-p-arg274ter), [ARID2 p.Gln920Ter](/variant/arid2-p-gln920ter), [ARID2 p.Ala1335Glu](/variant/arid2-p-ala1335glu).

### 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 1302414). 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.*