Is ERAP2 p.Thr256Ala (c.766A>G) pathogenic?

ERAP2 p.Thr256Ala (c.766A>G) is classified Uncertain significance in ERAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-01). AlphaMissense: likely benign (0.2612); Very rare (popmax 0.00513%, amr).

How common is ERAP2 p.Thr256Ala (c.766A>G) in the general population?

ERAP2 p.Thr256Ala (c.766A>G) is very rare (popmax 0.00513%, amr) (gnomAD).

What do computational predictors say about ERAP2 p.Thr256Ala (c.766A>G)?

AlphaMissense predicts likely benign (score 0.2612) — an in-silico prediction, not a clinical call.

ERAP2 p.Thr256Ala

c.766A>G · VCV4250397

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2612 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00513%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2612	likely benign
REVEL	0.267	benign-leaning
SaProt	LLR -7.28	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4	GERP 1, phastCons 0.68
Regional constraint	o/e 0.99	unconstrained · MANE · 30 kb · p 0.75 · regional, not allelic
Overall
CADD	22.8	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

Grpmax group 0.00513% Admixed American · 3/58,462 alleles

Filtering AF 0.00136% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000678%

Overall 0.000193% 3/1,553,348 alleles · very rare

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: ERAP2
Protein: p.Thr256Ala
Coding: c.766A>G
MANE Select: NM_001040458 · reported on NM_022350
Type: single nucleotide variant
Location: chr5:96886706 (GRCh38)

Full ERAP2 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/erap2-p-thr256ala (accessed [today's date]).

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