Is EEF1D p.Asp252= (c.756C>T) pathogenic?

EEF1D p.Asp252= (c.756C>T) is classified Likely benign in EEF1D (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-28). Very rare (popmax 0.00721%, nfe); Associated with EEF1D-related disorder.

What condition is associated with EEF1D p.Asp252= (c.756C>T)?

EEF1D p.Asp252= (c.756C>T) is associated with EEF1D-related disorder (ClinVar).

How common is EEF1D p.Asp252= (c.756C>T) in the general population?

EEF1D p.Asp252= (c.756C>T) is very rare (popmax 0.00721%, nfe) (gnomAD).

EEF1D p.Asp252=

c.756C>T · rs374067636 · VCV3045543

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00721%, nfe)

Conditions

EEF1D-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.4	GERP -2.7
Overall
CADD	4.562	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00721% European (non-Finnish) · 84/1,164,562 alleles

Filtering AF 0.00595% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00548%

Overall 0.00606% 96/1,584,328 alleles · very rare exomes 92/1,431,998 · genomes 4/152,330 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00721%	13,864
African / African-American	0.00672%	14,874
Remaining individualsnot grpmax-eligible	0.00491%	20,360
Finnishnot grpmax-eligible	0.00331%	30,198
Admixed American	0.00175%	57,010
South Asian	0.00114%	87,770

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.Asp252=
Coding: c.756C>T
MANE Select: NM_001130053
dbSNP: rs374067636
Type: single nucleotide variant
Location: chr8:143589326 (GRCh38)
Gene constraint: LOEUF 1.085 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.66 · 4 PDB
Residue 252: the 'catalytic (gef)' region; a turn; a UniProt-annotated variant site (in nedtchal; likely pathogenic)

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

Disease context

EEF1D-related disorder

Similar variants

EEF1D p.Asp386Asn Uncertain significance ★★ ⚠ same condition
EEF1D p.Arg292Ter Likely pathogenic ★ same condition
EEF1D p.Gln610Ter Likely pathogenic ★ same condition
EEF1D c.1288-10T>C Likely benign same condition
EEF1D p.Ala35= Likely benign same condition
EEF1D p.Ala549Ser Likely benign same condition
EEF1D p.Ala578= Benign same condition
EEF1D p.Arg110= Benign same condition

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-asp252 (accessed [today's date]).

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