# NM_001958.5(EEF1A2):c.999G>A (p.Pro333=)

https://sugi.bio/variant/eef1a2-p-pro333

## Summary

**EEF1A2 p.Pro333= (c.999G>A)** is classified **Likely benign** in EEF1A2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-02-16). Ultra-rare (popmax 0.0178%, eas); Associated with developmental and epileptic encephalopathy, 33.

**At a glance:** Likely benign · review: Multiple submitters · rsID rs760721599 · 3 submitters · 1 linked condition · ultra-rare (popmax 0.0178%, eas)

## For patients & families {#patients}

This is a change in the EEF1A2 gene that is classified as likely benign — not considered disease-causing, submitted by 3 submitters, and is linked to developmental and epileptic encephalopathy, 33.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant, Autosomal recessive, Not applicable |
| Age of onset (of this condition) | Infancy, Neonatal |
| Diagnostic panels | EEF1A2 is a diagnostic-grade gene on 7 Genomics England panels |

**Commonly reported features of Non-specific early-onset epileptic encephalopathy** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Encephalopathy — Very frequent (99-80%)
- Delayed speech and language development — Frequent (79-30%)
- Intellectual disability — Frequent (79-30%)
- Seizure — Frequent (79-30%)
- Global developmental delay — Frequent (79-30%)
- Hyporeflexia — Frequent (79-30%)
- Generalized hypotonia — Frequent (79-30%)
- Failure to thrive — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0016106/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [EEF1A2](https://sugi.bio/atlas/gene/EEF1A2/) |
| Protein change (HGVS p.) | p.Pro333= |
| Coding change (HGVS c.) | c.999G>A |
| MANE Select transcript | [NM_001958](https://www.ncbi.nlm.nih.gov/nuccore/NM_001958) |
| dbSNP | [rs760721599](https://www.ncbi.nlm.nih.gov/snp/rs760721599/) |
| Variant type | single nucleotide variant |
| Location | chr20:63490509-63490509 (GRCh38) |
| ClinVar | [VCV508914](https://www.ncbi.nlm.nih.gov/clinvar/variation/508914/) |

**All HGVS expressions:** `NC_000020.10:g.62121862C>T`, `NC_000020.11:g.63490509C>T`, `NG_034083.1:g.13807G>A`, `NM_001958.5:c.999G>A`

## 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 -20, GERP -3.79 — fast-evolving / accelerated position
- CADD: **PHRED 0.046**. 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, Δ0.23 donor 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 **0.0178%** (eas) · FAF95 0.00921% · FAF99 0.00722% · 8/44,870 in the highest group · 37/1,611,696 alleles overall — ultra-rare (popmax 0.0178%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.0178% | 5,609 |
| African / African-American | 0.016% | 6,245 |
| Remaining individuals (not grpmax-eligible) | 0.00481% | 20,797 |
| Admixed American | 0.00167% | 59,992 |
| European (non-Finnish) | 0.0011% | 90,709 |

*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}

**EEF1A2** population constraint: LOEUF 0.314, pLI 0.99995, missense-Z 6.0642; ClinGen dosage — haploinsufficiency 0, 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):

- **complex neurodevelopmental disorder** — Definitive (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 88.70, 59% of residues very-high.

**2 experimental structure(s)** (PDB): [8B6Z](https://www.rcsb.org/structure/8B6Z), [3C5J](https://www.rcsb.org/structure/3C5J).

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

*Describes the biological roles of EEF1A2 (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:** EEF1A2's established molecular role includes protein kinase binding.


### Pathways affected {#pathways}

EEF1A2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Eukaryotic Translation Elongation](https://reactome.org/content/detail/R-HSA-156842) | electronic |

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

**Molecular function:** protein kinase binding.

**Biological process:** positive regulation of lipid kinase activity.

## Clinical significance {#significance}

**Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-02-16.

**Submitter consensus:** unanimous (3/3 Likely benign).

**Submission history:** 3 submissions (2017–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Likely benign | criteria provided, single submitter | clinical testing | 2017-04-13 |
| Laboratory of Genetics, Children's Clinical University Hospital Latvia | Likely benign | criteria provided, single submitter | clinical testing | 2025-02-16 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2023-09-27 |

## Associated conditions {#conditions}

[developmental and epileptic encephalopathy, 33](https://sugi.bio/atlas/disease/developmental-and-epileptic-encephalopathy-33/).

**Reported phenotype names (ClinVar):** Developmental and epileptic encephalopathy, 33, not specified, Epileptic encephalopathy, early infantile, 33, AllHighlyPenetrant.

## Similar variants {#similar}

Related EEF1A2 variant pages (same residue, condition, or type): [EEF1A2 p.Pro333Arg](/variant/eef1a2-p-pro333arg), [EEF1A2 p.Arg266Trp](/variant/eef1a2-p-arg266trp), [EEF1A2 p.Arg423Cys](/variant/eef1a2-p-arg423cys), [EEF1A2 p.Arg69Cys](/variant/eef1a2-p-arg69cys), [EEF1A2 p.Asp91Asn](/variant/eef1a2-p-asp91asn), [EEF1A2 p.Asp97Asn](/variant/eef1a2-p-asp97asn), [EEF1A2 p.Glu122Lys](/variant/eef1a2-p-glu122lys), [EEF1A2 p.Glu124Lys](/variant/eef1a2-p-glu124lys).

### 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 508914). 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.*