Is EID3 p.Arg55Leu (c.164G>T) pathogenic?

EID3 p.Arg55Leu (c.164G>T) is classified Uncertain significance in EID3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-01). AlphaMissense: ambiguous (0.3786); Absent from gnomAD v4.1.

How common is EID3 p.Arg55Leu (c.164G>T) in the general population?

EID3 p.Arg55Leu (c.164G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EID3 p.Arg55Leu (c.164G>T)?

AlphaMissense predicts ambiguous (score 0.3786) — an in-silico prediction, not a clinical call.

EID3 p.Arg55Leu

c.164G>T · VCV4247631

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3786 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.3786	ambiguous
REVEL	0.45	indeterminate
SaProt	LLR -11.08	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.5	GERP 1.1, phastCons 1
Regional constraint	o/e 1.15	unconstrained · MANE · 998 bp · p 0.0026 · regional, not allelic
Overall
CADD	25.0	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

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: EID3
Protein: p.Arg55Leu
Coding: c.164G>T
MANE Select: NM_001008394
Type: single nucleotide variant
Location: chr12:104304098 (GRCh38)
Gene constraint: LOEUF 1.908 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.67 · 3 PDB

Full EID3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EID3 p.Ala153Pro Uncertain significance ★ ⚠ same type
EID3 p.Ala216Val Uncertain significance ★ ⚠ same type
EID3 p.Ala319Val Uncertain significance ★ ⚠ same type
EID3 p.Ala326Val Uncertain significance ★ ⚠ same type
EID3 p.Ala62Val Uncertain significance ★ ⚠ same type
EID3 p.Ala9Pro Uncertain significance ★ ⚠ same type
EID3 p.Arg179Leu Uncertain significance ★ ⚠ same type
EID3 p.Asn115Asp 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/eid3-p-arg55leu (accessed [today's date]).

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