Is EID3 p.Arg55Pro (c.164G>C) pathogenic?

EID3 p.Arg55Pro (c.164G>C) is classified Uncertain significance in EID3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-30). AlphaMissense: likely pathogenic (0.5736); Absent from gnomAD v4.1.

How common is EID3 p.Arg55Pro (c.164G>C) in the general population?

EID3 p.Arg55Pro (c.164G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EID3 p.Arg55Pro (c.164G>C)?

AlphaMissense predicts likely pathogenic (score 0.5736) — an in-silico prediction, not a clinical call.

EID3 p.Arg55Pro

c.164G>C · VCV4247633

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5736 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.5736	likely pathogenic
REVEL	0.53	indeterminate
SaProt	LLR -11.82	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
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	25.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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.Arg55Pro
Coding: c.164G>C
MANE Select: NM_001093771 · reported on NM_001008394
Type: single nucleotide variant
Location: chr12:104304098 (GRCh38)

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

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-arg55pro (accessed [today's date]).

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