Is EIF2AK2 p.Arg241= (c.723A>G) pathogenic?

EIF2AK2 p.Arg241= (c.723A>G) is classified Likely benign in EIF2AK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-03). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with EIF2AK2 p.Arg241= (c.723A>G)?

EIF2AK2 p.Arg241= (c.723A>G) is associated with Inborn genetic diseases (ClinVar).

How common is EIF2AK2 p.Arg241= (c.723A>G) in the general population?

EIF2AK2 p.Arg241= (c.723A>G) is absent from gnomAD v4.1 (gnomAD).

EIF2AK2 p.Arg241=

c.723A>G · VCV4618308

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

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 0.25	GERP -2.9, phastCons 0.091
Overall
CADD	5.554	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EIF2AK2
Protein: p.Arg241=
Coding: c.723A>G
MANE Select: NM_001135651
Type: single nucleotide variant
Location: chr2:37135546 (GRCh38)
Gene constraint: LOEUF 0.735 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.52 · 12 PDB

Full EIF2AK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EIF2AK2 p.Arg241Ile Uncertain significance ★ ⚠ same residue
EIF2AK2 p.Arg548Gln Uncertain significance ★★ ⚠ same condition
EIF2AK2 p.Asn230Ser Uncertain significance ★★ ⚠ same condition
EIF2AK2 p.Ile215Met Uncertain significance ★★ ⚠ same condition
EIF2AK2 p.Lys238Gln Uncertain significance ★★ ⚠ same condition
EIF2AK2 p.Met252Val Uncertain significance ★★ ⚠ same condition
EIF2AK2 p.Ser438Cys Uncertain significance ★★ ⚠ same condition
EIF2AK2 p.Ser92Tyr Uncertain significance ★★ ⚠ 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/eif2ak2-p-arg241 (accessed [today's date]).

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