Is EFTUD2 p.Arg413His (c.1238G>A) pathogenic?

EFTUD2 p.Arg413His (c.1238G>A) is classified Conflicting classifications of pathogenicity in EFTUD2 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-10-24). AlphaMissense: ambiguous (0.3909); Ultra-rare (popmax 0.0116%, nfe); Associated with Inborn genetic diseases.

What condition is associated with EFTUD2 p.Arg413His (c.1238G>A)?

EFTUD2 p.Arg413His (c.1238G>A) is associated with Inborn genetic diseases (ClinVar).

How common is EFTUD2 p.Arg413His (c.1238G>A) in the general population?

EFTUD2 p.Arg413His (c.1238G>A) is ultra-rare (popmax 0.0116%, nfe) (gnomAD).

What do computational predictors say about EFTUD2 p.Arg413His (c.1238G>A)?

AlphaMissense predicts ambiguous (score 0.3909) — an in-silico prediction, not a clinical call.

EFTUD2 p.Arg413His

c.1238G>A · VCV3706531

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.3909 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0116%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3909	ambiguous
REVEL	0.523	indeterminate
SaProt	LLR -12.81	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 19 kb · p 1.7e-08 · regional, not allelic
Overall
CADD	26.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0116% European (non-Finnish) · 137/1,180,048 alleles

Filtering AF 0.01% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00939%

Overall 0.00861% 139/1,614,002 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0116%	8,613
East Asian	0.00223%	44,892
Remaining individualsnot grpmax-eligible	0.0016%	62,488

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: EFTUD2
Protein: p.Arg413His
Coding: c.1238G>A
MANE Select: NM_004247
Type: single nucleotide variant
Location: chr17:44864977 (GRCh38)
Gene constraint: LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 89.94 · 72 PDB
Residue 413: an α-helix

Full EFTUD2 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

EFTUD2 c.1058+1G>A Pathogenic ★★ same condition
EFTUD2 c.702+1G>T Pathogenic/Likely pathogenic ★★ same condition
EFTUD2 p.Arg354Ter Pathogenic/Likely pathogenic ★★ same condition
EFTUD2 c.2347+3A>G Uncertain significance ★★ same condition
EFTUD2 p.Arg495Gln Uncertain significance ★★ ⚠ same condition
EFTUD2 p.Arg529Cys Uncertain significance ★★ ⚠ same condition
EFTUD2 p.Asn125Asp Uncertain significance ★★ ⚠ same condition
EFTUD2 p.Asn548Ser 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/eftud2-p-arg413his (accessed [today's date]).

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