# NM_000070.3(CAPN3):c.1437C>T (p.Ser479=)

https://sugi.bio/variant/capn3-p-ser479

## Summary

**CAPN3 p.Ser479= (c.1437C>T)** is classified **Conflicting classifications of pathogenicity** in CAPN3 (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2026-01-24). Rare (popmax 0.851%, eas); Associated with Inborn genetic diseases.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs147914333 · 8 submitters · 2 linked conditions · rare (popmax 0.851%, eas)

## For patients & families {#patients}

This is a change in the CAPN3 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 8 submitters, and is linked to Inborn genetic diseases.

*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 | [CAPN3](https://sugi.bio/atlas/gene/CAPN3/) |
| Protein change (HGVS p.) | p.Ser479= |
| Coding change (HGVS c.) | c.1437C>T |
| MANE Select transcript | [NM_000070](https://www.ncbi.nlm.nih.gov/nuccore/NM_000070) |
| dbSNP | [rs147914333](https://www.ncbi.nlm.nih.gov/snp/rs147914333/) |
| Variant type | single nucleotide variant |
| Location | chr15:42401723-42401723 (GRCh38) |
| ClinVar | [VCV497380](https://www.ncbi.nlm.nih.gov/clinvar/variation/497380/) |

**All HGVS expressions:** `LRG_849:g.58621C>T`, `LRG_849t1:c.1437C>T`, `NC_000015.10:g.42401723C>T`, `NC_000015.9:g.42693921C>T`, `NG_008660.1:g.58621C>T`, `NM_000070.3:c.1437C>T`, `NM_024344.2:c.1437C>T`, `NM_173087.2:c.1293C>T`

## 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 2.661, GERP -3.48, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 12.95**. 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: **below the reporting threshold**. This position is scored for a different substitution (C>G, Δ0.61 acceptor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.851%** (eas) · FAF95 0.781% · FAF99 0.753% · 382/44,884 in the highest group · 419/1,614,190 alleles overall — rare (popmax 0.851%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.851% | 117 |
| South Asian | 0.0285% | 3,503 |
| Remaining individuals (not grpmax-eligible) | 0.0128% | 7,813 |
| European (non-Finnish) | 0.000254% | 393,337 |

*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}

**CAPN3** population constraint: LOEUF 0.896, pLI 5.2262e-19, missense-Z 0.86012; ClinGen dosage — haploinsufficiency 30, 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):

- **muscular dystrophy, limb-girdle, autosomal dominant** — Definitive (AD)
- **autosomal recessive limb-girdle muscular dystrophy** — Definitive (AR)

## Protein context {#protein}

Residue **479** lies in the 'domain iii' region; a UniProt-annotated variant site (in lgmdr1).

AlphaFold model confidence (whole protein): pLDDT 79.18, 44% of residues very-high.

**5 experimental structure(s)** (PDB): [4OKH](https://www.rcsb.org/structure/4OKH), [6BDT](https://www.rcsb.org/structure/6BDT), [6BGP](https://www.rcsb.org/structure/6BGP), [6BJD](https://www.rcsb.org/structure/6BJD), [6BKJ](https://www.rcsb.org/structure/6BKJ) — incl. mutant structure 6BDT.

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

*Describes the biological roles of CAPN3 (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:** CAPN3's established molecular role includes catalytic activity. p.Ser479= falls in the domain iii region.


### Pathways affected {#pathways}

CAPN3 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Degradation of the extracellular matrix](https://reactome.org/content/detail/R-HSA-1474228) | curated |

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

**Molecular function:** catalytic activity, peptidase activity, cysteine-type peptidase activity, titin binding, identical protein binding.

**Biological process:** proteolysis, protein catabolic process, protein destabilization, negative regulation of protein sumoylation, negative regulation of apoptotic process, regulation of canonical NF-kappaB signal transduction.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2026-01-24.

**Submitter consensus:** conflicting (4 Likely benign, 3 Uncertain significance, 1 Benign).

**Submission history:** 8 submissions (2016–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2017-04-27 |
| Natera, Inc. | Likely benign | no assertion criteria provided | clinical testing | 2020-04-17 |
| Eurofins Ntd Llc (ga) | Uncertain significance | criteria provided, single submitter | clinical testing | 2016-11-29 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-01-24 |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-02-02 |
| Revvity Omics, Revvity | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-04-13 |
| CeGaT Center for Human Genetics Tuebingen | Likely benign | criteria provided, single submitter | clinical testing | 2024-09-01 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-27 |

## Associated conditions {#conditions}

[Inborn genetic diseases](https://sugi.bio/atlas/disease/inborn-genetic-diseases/), [autosomal recessive limb-girdle muscular dystrophy type 2A](https://sugi.bio/atlas/disease/autosomal-recessive-limb-girdle-muscular-dystrophy-type-2a/).

**Reported phenotype names (ClinVar):** Inborn genetic diseases, not provided, Autosomal recessive limb-girdle muscular dystrophy type 2A, not specified, AllHighlyPenetrant, none provided, Calpainopathy, Muscular dystrophy, limb-girdle, type 2A, Amish, LEYDEN-MOEBIUS MUSCULAR DYSTROPHY, MUSCULAR DYSTROPHY, PELVOFEMORAL.

## Same-residue context {#hotspot}

Residue **479** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [CAPN3 p.Ser479Gly](/variant/capn3-p-ser479gly). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related CAPN3 variant pages (same residue, condition, or type): [CAPN3 p.Ser479Gly](/variant/capn3-p-ser479gly), [CAPN3 c.1115+5G>C](/variant/capn3-c-1115-plus-5g-c), [CAPN3 c.1194-2A>G](/variant/capn3-c-1194-minus-2a-g), [CAPN3 c.1194-9A>G](/variant/capn3-c-1194-minus-9a-g), [CAPN3 c.1746-20C>G](/variant/capn3-c-1746-minus-20c-g), [CAPN3 c.1993-1G>A](/variant/capn3-c-1993-minus-1g-a), [CAPN3 c.499-1G>A](/variant/capn3-c-499-minus-1g-a), [CAPN3 p.Ala702Val](/variant/capn3-p-ala702val).

### 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 497380). 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.*