# NM_001103.4(ACTN2):c.776C>T (p.Ala259Val)

https://sugi.bio/variant/actn2-p-ala259val

## Summary

**ACTN2 p.Ala259Val (c.776C>T)** is classified **Uncertain significance** in ACTN2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-09-17). AlphaMissense: likely pathogenic (0.5642); Ultra-rare (popmax 0.0165%, mid); Associated with dilated cardiomyopathy 1AA.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs566552494 · 4 submitters · 4 linked conditions · AlphaMissense likely pathogenic · ultra-rare (popmax 0.0165%, mid)

## For patients & families {#patients}

This is a change in the ACTN2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 4 submitters, and is linked to dilated cardiomyopathy 1AA.

*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.*

|  |  |
| --- | --- |
| Diagnostic panels | ACTN2 is a diagnostic-grade gene on 10 Genomics England panels |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0015543/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [ACTN2](https://sugi.bio/atlas/gene/ACTN2/) |
| Protein change (HGVS p.) | p.Ala259Val |
| Coding change (HGVS c.) | c.776C>T |
| MANE Select transcript | [NM_001103](https://www.ncbi.nlm.nih.gov/nuccore/NM_001103) |
| dbSNP | [rs566552494](https://www.ncbi.nlm.nih.gov/snp/rs566552494/) |
| Variant type | single nucleotide variant |
| Location | chr1:236735713-236735713 (GRCh38) |
| ClinVar | [VCV463217](https://www.ncbi.nlm.nih.gov/clinvar/variation/463217/) |

**All HGVS expressions:** `LRG_436:g.76573C>T`, `LRG_436t1:c.776C>T`, `NC_000001.10:g.236899013C>T`, `NC_000001.11:g.236735713C>T`, `NG_009081.2:g.76573C>T`, `NM_001103.4:c.776C>T`, `NM_001278343.2:c.783+1195C>T`, `NM_001278344.2:c.41C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.5642)
- REVEL 0.593 (indeterminate)
- SaProt LLR -11.262 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this damaging; REVEL makes no call
- Conservation: phyloP 7.666, GERP 2.4, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 28.7**. 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 0.65** across the covering region of the MANE Select transcript (236,686,733–236,737,189), spanning 50,456 bp. Chi-square p 1.6e-10. 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 (gnomAD v4.1): grpmax **0.0165%** (mid) · FAF95 0.00122% · FAF99 0.00104% · 1/6,062 in the highest group · 25/1,614,120 alleles overall — ultra-rare (popmax 0.0165%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Middle Eastern (grpmax) | 0.0165% | 6,062 |
| European (non-Finnish) | 0.00186% | 53,636 |
| African / African-American | 0.00133% | 75,044 |
| South Asian | 0.0011% | 91,086 |

*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}

**ACTN2** population constraint: LOEUF 0.432, pLI 0.99996, missense-Z 2.2746. *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):

- **ACTN2-related cardiac and skeletal myopathy** — Definitive (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 84.88, 47% of residues very-high.

**18 experimental structure(s)** (PDB): [1H8B](https://www.rcsb.org/structure/1H8B), [1HCI](https://www.rcsb.org/structure/1HCI), [1QUU](https://www.rcsb.org/structure/1QUU), [4D1E](https://www.rcsb.org/structure/4D1E), [5A36](https://www.rcsb.org/structure/5A36), [5A37](https://www.rcsb.org/structure/5A37) — incl. mutant structure 9SIR.

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

*Describes the biological roles of ACTN2 (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:** ACTN2's established molecular role includes phosphatidylinositol-4,5-bisphosphate binding.


### Pathways affected {#pathways}

ACTN2 participates in **9 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Platelet degranulation ](https://reactome.org/content/detail/R-HSA-114608) | curated |
| [RAF/MAP kinase cascade](https://reactome.org/content/detail/R-HSA-5673001) | curated |
| [Striated Muscle Contraction](https://reactome.org/content/detail/R-HSA-390522) | curated |
| [Assembly and cell surface presentation of NMDA receptors](https://reactome.org/content/detail/R-HSA-9609736) | electronic |
| [Long-term potentiation](https://reactome.org/content/detail/R-HSA-9620244) | electronic |
| [Negative regulation of NMDA receptor-mediated neuronal transmission](https://reactome.org/content/detail/R-HSA-9617324) | electronic |
| [Nephrin family interactions](https://reactome.org/content/detail/R-HSA-373753) | electronic |
| [Ras activation upon Ca2+ influx through NMDA receptor](https://reactome.org/content/detail/R-HSA-442982) | electronic |
| [Unblocking of NMDA receptors, glutamate binding and activation](https://reactome.org/content/detail/R-HSA-438066) | electronic |

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

**Molecular function:** phosphatidylinositol-4,5-bisphosphate binding, cytoskeletal protein binding, protein domain specific binding, titin binding, identical protein binding, transmembrane transporter binding.

**Biological process:** microspike assembly, regulation of membrane potential, negative regulation of potassium ion transport, positive regulation of potassium ion transport, sarcomere organization, focal adhesion assembly.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-09-17.

**Submitter consensus:** unanimous (4/4 Uncertain significance).

**Submission history:** 4 submissions (2021–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Uncertain significance | criteria provided, single submitter | clinical testing | 2021-06-28 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-01-16 |
| Fulgent Genetics, Fulgent Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2021-10-01 |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-09-17 |

## Associated conditions {#conditions}

[dilated cardiomyopathy 1AA](https://sugi.bio/atlas/disease/dilated-cardiomyopathy-1aa/), [familial hypertrophic cardiomyopathy](https://sugi.bio/atlas/disease/familial-hypertrophic-cardiomyopathy/), [myopathy, congenital, with structured cores and z-line abnormalities](https://sugi.bio/atlas/disease/myopathy-congenital-with-structured-cores-and-z-line-abnormalities/), [myopathy, distal, 6, adult-onset, autosomal dominant](https://sugi.bio/atlas/disease/myopathy-distal-6-adult-onset-autosomal-dominant/).

**Reported phenotype names (ClinVar):** Dilated cardiomyopathy 1AA, Primary familial hypertrophic cardiomyopathy, not provided, Cardiovascular phenotype, Myopathy, congenital, with structured cores and z-line abnormalities, Myopathy, distal, 6, adult-onset, autosomal dominant, none provided, Cardiomyopathy, dilated, 1AA, with or without LVNC, CARDIOMYOPATHY, DILATED, 1AA, WITH OR WITHOUT LEFT VENTRICULAR NONCOMPACTION, CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 23, WITH OR WITHOUT LEFT VENTRICULAR NONCOMPACTION.

## Similar variants {#similar}

Related ACTN2 variant pages (same residue, condition, or type): [ACTN2 p.Ala259Thr](/variant/actn2-p-ala259thr), [ACTN2 p.Ala259=](/variant/actn2-p-ala259), [ACTN2 p.Ala119Thr](/variant/actn2-p-ala119thr), [ACTN2 p.Leu727Arg](/variant/actn2-p-leu727arg), [ACTN2 p.Thr247Met](/variant/actn2-p-thr247met), [ACTN2 c.1107+3G>A](/variant/actn2-c-1107-plus-3g-a), [ACTN2 c.1108-10A>G](/variant/actn2-c-1108-minus-10a-g), [ACTN2 c.1255+1G>C](/variant/actn2-c-1255-plus-1g-c).

### 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 463217). 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.*