Is EIF4A2 p.Asp37del (c.106GAT[1]) pathogenic?

EIF4A2 p.Asp37del (c.106GAT[1]) is classified Likely pathogenic in EIF4A2 (ClinVar, No assertion criteria, 1 submitter). Very rare (popmax 8.47e-05%, nfe); Associated with neurodevelopmental disorder.

What condition is associated with EIF4A2 p.Asp37del (c.106GAT[1])?

EIF4A2 p.Asp37del (c.106GAT[1]) is associated with neurodevelopmental disorder (ClinVar).

How common is EIF4A2 p.Asp37del (c.106GAT[1]) in the general population?

EIF4A2 p.Asp37del (c.106GAT[1]) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

EIF4A2 p.Asp37del

c.106GAT[1] · rs1171371205 · VCV1712515

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

neurodevelopmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5	GERP 1.8, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,028 alleles

Overall 0.000137% 2/1,461,882 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0016%	62,510
European (non-Finnish)grpmax	8.47e-05%	1,180,027

Remaining individuals 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: EIF4A2
Protein: p.Asp37del
Coding: c.106GAT[1]
MANE Select: NM_001967
dbSNP: rs1171371205
Type: Microsatellite
Location: chr3:186784593 (GRCh38)
Gene constraint: LOEUF 0.298 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 86.94 · 1 PDB
Residue 37: a UniProt-annotated variant site (in nedhss; uncertain significance); an α-helix

Full EIF4A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EIF4A2 p.Leu44fs Likely pathogenic ★★ same condition
EIF4A2 p.Asp37Val Uncertain significance ★ ⚠ same residue
EIF4A2 p.Gly161Trp Likely pathogenic ★ same condition
EIF4A2 p.Thr216Ala Pathogenic ★ same condition
EIF4A2 p.Thr216Ile Pathogenic ★ same condition
EIF4A2 p.Ile315del Likely pathogenic same condition
EIF4A2 p.Leu344Phe Pathogenic/Likely pathogenic same condition
EIF4A2 p.Ser214Tyr Likely pathogenic 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/eif4a2-p-asp37del (accessed [today's date]).

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