Is EEF1D p.Arg288Trp (c.862C>T) pathogenic?

EEF1D p.Arg288Trp (c.862C>T) is classified Likely benign in EEF1D (ClinVar, Single submitter, 3 submitters; last evaluated 2025-05-01). Rare (popmax 0.348%, nfe).

How common is EEF1D p.Arg288Trp (c.862C>T) in the general population?

EEF1D p.Arg288Trp (c.862C>T) is rare (popmax 0.348%, nfe) (gnomAD).

EEF1D p.Arg288Trp

c.862C>T · rs78886866 · VCV3038727

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.348%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.045	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.3	GERP -1.1, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 10 kb · p 0.79 · regional, not allelic
Overall
CADD	18.15	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.348% European (non-Finnish) · 4,048/1,162,034 alleles

Filtering AF 0.339% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.336%

Overall 0.281% 4,449/1,581,002 alleles · rare exomes 4,178/1,428,692 · genomes 271/152,310 · joint denominator

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	1.32%	76
European (non-Finnish)grpmax	0.348%	287
Ashkenazi Jewishnot grpmax-eligible	0.296%	338
Remaining individualsnot grpmax-eligible	0.195%	512
Finnishnot grpmax-eligible	0.144%	696
Middle Eastern	0.118%	849
African / African-American	0.0712%	1,405
Admixed American	0.0374%	2,676
South Asian	0.0182%	5,490
East Asian	0.00457%	21,890

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: EEF1D
Protein: p.Arg288Trp
Coding: c.862C>T
MANE Select: NM_001130053
dbSNP: rs78886866
Type: single nucleotide variant
Location: chr8:143589220 (GRCh38)
Gene constraint: LOEUF 1.085 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.66 · 4 PDB
Residue 288: a UniProt-annotated variant site (in nedtchal; likely pathogenic)

Full EEF1D gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EEF1D c.1905+1G>A Uncertain significance ★★ same type
EEF1D p.Arg585Cys Uncertain significance ★★ ⚠ same type
EEF1D p.Asp100Gly Uncertain significance ★★ same type
EEF1D p.Asp386Asn Uncertain significance ★★ ⚠ same type
EEF1D p.Gly351Ala Uncertain significance ★★ same type
EEF1D p.Pro350Leu Uncertain significance ★★ same type
EEF1D p.Ser213Asn Uncertain significance ★★ same type
EEF1D p.Thr575Met Uncertain significance ★★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/eef1d-p-arg288trp (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown