Is AIRE p.Pro280Ser (c.838C>T) pathogenic?

AIRE p.Pro280Ser (c.838C>T) is classified Uncertain significance in AIRE (ClinVar, Single submitter, 1 submitter; last evaluated 2026-06-05). AlphaMissense: likely benign (0.0766); Very rare (popmax 0.0022%, sas).

How common is AIRE p.Pro280Ser (c.838C>T) in the general population?

AIRE p.Pro280Ser (c.838C>T) is very rare (popmax 0.0022%, sas) (gnomAD).

What do computational predictors say about AIRE p.Pro280Ser (c.838C>T)?

AlphaMissense predicts likely benign (score 0.0766) — an in-silico prediction, not a clinical call.

AIRE p.Pro280Ser

c.838C>T · rs2517880829 · VCV2504735

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0766 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0766	likely benign
REVEL	0.305	indeterminate
SaProt	LLR -7.27	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.26	GERP -2.6
Regional constraint	o/e 0.97	unconstrained · MANE · 5,090 bp · p 0.58 · regional, not allelic
Overall
CADD	7.393	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 0.0022% South Asian · 2/90,892 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000137% 2/1,459,240 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: AIRE
Protein: p.Pro280Ser
Coding: c.838C>T
MANE Select: NM_000383
dbSNP: rs2517880829
Type: single nucleotide variant
Location: chr21:44290027 (GRCh38)
Gene constraint: LOEUF 1.169 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.30 · 4 PDB
Residue 280: the sand domain; the 'disordered' region

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

Similar variants

AIRE p.Pro280= Likely benign ★ same residue
AIRE c.1095+2T>C Pathogenic/Likely pathogenic ★★ same type
AIRE c.1096-1G>A Pathogenic ★★ same type
AIRE c.1278+1G>A Likely pathogenic ★★ same type
AIRE c.1279-2A>G Likely pathogenic ★★ same type
AIRE c.1503+1G>A Likely pathogenic ★★ same type
AIRE c.1503+1G>T Pathogenic/Likely pathogenic ★★ same type
AIRE c.463+2T>C Pathogenic/Likely pathogenic ★★ 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/aire-p-pro280ser (accessed [today's date]).

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