Is IRF2BP2 p.Ala3= (c.9G>A) pathogenic?

IRF2BP2 p.Ala3= (c.9G>A) is classified Likely benign in IRF2BP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-15). No allele count reported in gnomAD v4.1 (AN 1,499,240).

How common is IRF2BP2 p.Ala3= (c.9G>A) in the general population?

IRF2BP2 p.Ala3= (c.9G>A) is no allele count reported in gnomAD v4.1 (AN 1,499,240) (gnomAD).

IRF2BP2 p.Ala3=

c.9G>A · rs2528525166 · VCV2828817

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,499,240)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.43	GERP 0.25, phastCons 1
Overall
CADD	12.57	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,499,240). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: IRF2BP2
Protein: p.Ala3=
Coding: c.9G>A
MANE Select: NM_182972
dbSNP: rs2528525166
Type: single nucleotide variant
Location: chr1:234609486 (GRCh38)
Gene constraint: LOEUF 0.709 · pLI 0.41 (gnomAD)
Structure: AlphaFold pLDDT 56.84 · 3 PDB

Full IRF2BP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IRF2BP2 p.Ala3Gly Uncertain significance ★ ⚠ same residue
IRF2BP2 p.Ala3_Ala4dup Uncertain significance ★★ same residue
IRF2BP2 p.Ala3_Ala4del Uncertain significance ★ same residue
IRF2BP2 p.Ala143Gly Uncertain significance ★★ ⚠ same type
IRF2BP2 p.Ala209Gly Uncertain significance ★★ ⚠ same type
IRF2BP2 p.Ala214Thr Uncertain significance ★★ ⚠ same type
IRF2BP2 p.Ala246Val Uncertain significance ★★ ⚠ same type
IRF2BP2 p.Ala254Thr 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/irf2bp2-p-ala3 (accessed [today's date]).

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