Is EID2B p.Gln83Pro (c.248A>C) pathogenic?

EID2B p.Gln83Pro (c.248A>C) is classified Uncertain significance in EID2B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-23). AlphaMissense: likely benign (0.1362); Absent from gnomAD v4.1.

How common is EID2B p.Gln83Pro (c.248A>C) in the general population?

EID2B p.Gln83Pro (c.248A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EID2B p.Gln83Pro (c.248A>C)?

AlphaMissense predicts likely benign (score 0.1362) — an in-silico prediction, not a clinical call.

EID2B p.Gln83Pro

c.248A>C · VCV3844029

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1362 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1362	likely benign
REVEL	0.036	moderately benign-leaning
SaProt	LLR -8.03	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.34	GERP -2.3
Regional constraint	o/e 1.03	unconstrained · MANE · 482 bp · p 0.69 · regional, not allelic
Overall
CADD	8.051	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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: EID2B
Protein: p.Gln83Pro
Coding: c.248A>C
MANE Select: NM_152361
Type: single nucleotide variant
Location: chr19:39532555 (GRCh38)
Gene constraint: LOEUF 1.759 · pLI 0.24 (gnomAD)
Structure: AlphaFold pLDDT 70.26

Full EID2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EID2B p.Ala131Val Uncertain significance ★ ⚠ same type
EID2B p.Ala134Thr Uncertain significance ★ ⚠ same type
EID2B p.Ala143Ser Uncertain significance ★ ⚠ same type
EID2B p.Ala45Thr Uncertain significance ★ ⚠ same type
EID2B p.Ala45Val Uncertain significance ★ ⚠ same type
EID2B p.Arg119Lys Uncertain significance ★ ⚠ same type
EID2B p.Gln84Arg Uncertain significance ★ ⚠ same type
EID2B p.Glu123Val 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/eid2b-p-gln83pro (accessed [today's date]).

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