Is IRF7 p.Pro308Ser (c.922C>T) pathogenic?

IRF7 p.Pro308Ser (c.922C>T) is classified Uncertain significance in IRF7 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-08-27). AlphaMissense: likely benign (0.1032); Very rare (popmax 0.00354%, nfe); Associated with immunodeficiency 39.

What condition is associated with IRF7 p.Pro308Ser (c.922C>T)?

IRF7 p.Pro308Ser (c.922C>T) is associated with immunodeficiency 39 (ClinVar).

How common is IRF7 p.Pro308Ser (c.922C>T) in the general population?

IRF7 p.Pro308Ser (c.922C>T) is very rare (popmax 0.00354%, nfe) (gnomAD).

What do computational predictors say about IRF7 p.Pro308Ser (c.922C>T)?

AlphaMissense predicts likely benign (score 0.1032) — an in-silico prediction, not a clinical call.

IRF7 p.Pro308Ser

Q: How is Predisposition to severe viral infection due to IRF7 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.922C>T · rs1263250882 · VCV577080

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1032 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00354%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

immunodeficiency 39

Computational evidence

Protein change
AlphaMissense	0.1032	likely benign
REVEL	0.268	benign-leaning
SaProt	LLR -5.62	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 1.2	phastCons 0.064
Regional constraint	o/e 1.24	unconstrained · MANE · 2,716 bp · p 9.3e-11 · regional, not allelic
Overall
CADD	10.48	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 0.00354% European (non-Finnish) · 41/1,157,420 alleles

Filtering AF 0.00264% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00237%

Overall 0.00275% 43/1,564,242 alleles · very rare exomes 42/1,412,356 · genomes 1/151,886 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00354%	28,230
Admixed American	0.00191%	52,344
Remaining individualsnot grpmax-eligible	0.00166%	60,386

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: IRF7
Protein: p.Pro308Ser
Coding: c.922C>T
MANE Select: NM_001572
dbSNP: rs1263250882
Type: single nucleotide variant
Location: chr11:613521 (GRCh38)
Gene constraint: LOEUF 1.766 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.10 · 1 PDB
Residue 308: a UniProt-annotated variant site (abolishes ifnb induction upon sendai virus infection); the 'necessary for the interaction with nmi' region

Full IRF7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency 39 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Predisposition to severe viral infection due to IRF7 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages

Similar variants

IRF7 p.Pro308Leu Uncertain significance ★ ⚠ same residue
IRF7 p.Pro308= Likely benign ★ same residue
IRF7 c.20+39G>C Uncertain significance ★★ same condition
IRF7 c.21-16G>A Uncertain significance ★★ same condition
IRF7 c.21-19C>T Uncertain significance ★★ same condition
IRF7 c.848-1G>C Uncertain significance ★★ same condition
IRF7 p.Ala145Thr Uncertain significance ★★ ⚠ same condition
IRF7 p.Ala251Pro Uncertain significance ★★ ⚠ same condition

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/irf7-p-pro308ser (accessed [today's date]).

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