# NM_001961.4(EEF2):c.1989C>T (p.Thr663=)

https://sugi.bio/variant/eef2-p-thr663

## Summary

**EEF2 p.Thr663= (c.1989C>T)** is classified **Benign/Likely benign** in EEF2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-06-29). Very rare (popmax 0.00659%, sas).

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs745451916 · 2 submitters · very rare (popmax 0.00659%, sas)

## For patients & families {#patients}

This is a change in the EEF2 gene that is classified as benign/likely benign — not considered disease-causing, submitted by 2 submitters.

*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 | [EEF2](https://sugi.bio/atlas/gene/EEF2/) |
| Protein change (HGVS p.) | p.Thr663= |
| Coding change (HGVS c.) | c.1989C>T |
| MANE Select transcript | [NM_001961](https://www.ncbi.nlm.nih.gov/nuccore/NM_001961) |
| dbSNP | [rs745451916](https://www.ncbi.nlm.nih.gov/snp/rs745451916/) |
| Variant type | single nucleotide variant |
| Location | chr19:3977897-3977897 (GRCh38) |
| ClinVar | [VCV1256088](https://www.ncbi.nlm.nih.gov/clinvar/variation/1256088/) |

**All HGVS expressions:** `NC_000019.10:g.3977897G>A`, `NC_000019.9:g.3977895G>A`, `NG_042274.1:g.12567C>T`, `NM_001961.4:c.1989C>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 -20, GERP -4.46 — fast-evolving / accelerated position
- CADD: **PHRED 0.088**. 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: **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 **0.00659%** (sas) · FAF95 0.00519% · FAF99 0.00474% · 6/91,060 in the highest group · 91/1,613,552 alleles overall — very rare (popmax 0.00659%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 0.00659% | 15,177 |
| Remaining individuals (not grpmax-eligible) | 0.0064% | 15,618 |
| European (non-Finnish) | 0.00636% | 15,733 |
| East Asian | 0.00446% | 22,439 |
| African / African-American | 0.004% | 24,976 |
| Admixed American | 0.00167% | 59,994 |

*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}

**EEF2** population constraint: LOEUF 0.39, pLI 0.99999, missense-Z 3.6054. *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):

- **spinocerebellar ataxia type 26** — Moderate (AD)

## Protein context {#protein}

Residue **663** lies in a β-strand.

AlphaFold model confidence (whole protein): pLDDT 89.97, 66% of residues very-high.

**26 experimental structure(s)** (PDB): [4V6X](https://www.rcsb.org/structure/4V6X), [6D9J](https://www.rcsb.org/structure/6D9J), [6Z6M](https://www.rcsb.org/structure/6Z6M), [6Z6N](https://www.rcsb.org/structure/6Z6N), [8XSX](https://www.rcsb.org/structure/8XSX), [8Y0W](https://www.rcsb.org/structure/8Y0W).

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

*Describes the biological roles of EEF2 (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:** EEF2's established molecular role includes RNA binding. In Reactome, EEF2 is annotated in disease pathway(s) including **Uptake and function of diphtheria toxin**.

**Disease mechanism (Reactome):** EEF2 loss or alteration is curated in [Uptake and function of diphtheria toxin](https://reactome.org/content/detail/R-HSA-5336415).

### Pathways affected {#pathways}

EEF2 participates in **5 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Uptake and function of diphtheria toxin](https://reactome.org/content/detail/R-HSA-5336415) | curated |
| [Neutrophil degranulation](https://reactome.org/content/detail/R-HSA-6798695) | curated |
| [Protein methylation](https://reactome.org/content/detail/R-HSA-8876725) | curated |
| [Peptide chain elongation](https://reactome.org/content/detail/R-HSA-156902) | electronic |
| [Synthesis of diphthamide-EEF2](https://reactome.org/content/detail/R-HSA-5358493) | electronic |

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

**Molecular function:** RNA binding, translation elongation factor activity, GTPase activity, protein kinase binding, ribosome binding, cadherin binding.

**Biological process:** translational elongation, positive regulation of translation.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2023-06-29.

**Submitter consensus:** conflicting (1 Benign, 1 Likely benign).

**Submission history:** 2 submissions (2020–2023); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Athena Diagnostics | Benign | criteria provided, single submitter | clinical testing | 2020-09-21 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2023-06-29 |

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

## Similar variants {#similar}

Related EEF2 variant pages (same residue, condition, or type): [EEF2 p.Ala237Thr](/variant/eef2-p-ala237thr), [EEF2 p.Ala238Thr](/variant/eef2-p-ala238thr), [EEF2 p.Ala338Gly](/variant/eef2-p-ala338gly), [EEF2 p.Ala624Thr](/variant/eef2-p-ala624thr), [EEF2 p.Ala808Val](/variant/eef2-p-ala808val), [EEF2 p.Arg633His](/variant/eef2-p-arg633his), [EEF2 p.Arg647His](/variant/eef2-p-arg647his), [EEF2 p.Arg726Trp](/variant/eef2-p-arg726trp).

### 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 1256088). 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.*