Is IL1RN p.Asp112= (c.336C>T) pathogenic?

IL1RN p.Asp112= (c.336C>T) is classified Conflicting classifications of pathogenicity in IL1RN (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-04-14). Ultra-rare (popmax 0.033%, mid); Associated with autoinflammatory syndrome.

What condition is associated with IL1RN p.Asp112= (c.336C>T)?

IL1RN p.Asp112= (c.336C>T) is associated with autoinflammatory syndrome, sterile multifocal osteomyelitis with periostitis and pustulosis (ClinVar).

How common is IL1RN p.Asp112= (c.336C>T) in the general population?

IL1RN p.Asp112= (c.336C>T) is ultra-rare (popmax 0.033%, mid) (gnomAD).

IL1RN p.Asp112=

c.336C>T · rs751937390 · VCV1121683

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.033%, mid)

Conditions

autoinflammatory syndrome

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 -0.24	GERP 0.78, phastCons 0.062
Overall
CADD	4.716	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.033% Middle Eastern · 2/6,062 alleles

Filtering AF 0.00582% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00242%

Overall 0.00155% 25/1,614,220 alleles · ultra-rare exomes 25/1,461,886 · genomes 0/152,334 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.0032%	31,256
South Asian	0.0022%	45,546
European (non-Finnish)	0.00153%	65,558
African / African-American	0.00133%	75,056

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: IL1RN
Protein: p.Asp112=
Coding: c.336C>T
MANE Select: NM_173842
dbSNP: rs751937390
Type: single nucleotide variant
Location: chr2:113132673 (GRCh38)
Gene constraint: LOEUF 1.507 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.98 · 5 PDB
Residue 112: an α-helix

Full IL1RN gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autoinflammatory syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: sterile multifocal osteomyelitis with periostitis and pustulosis

Similar variants

IL1RN p.Glu77Ter Pathogenic ★★ same condition
IL1RN p.Ser21= Likely pathogenic ★★ same condition
IL1RN c.*119C>T Uncertain significance ★★ same condition
IL1RN p.Ala140Thr Uncertain significance ★★ ⚠ same condition
IL1RN p.Ala2Thr Uncertain significance ★★ same condition
IL1RN p.Arg102Thr Uncertain significance ★★ ⚠ same condition
IL1RN p.Arg127Cys Uncertain significance ★★ ⚠ same condition
IL1RN p.Arg26Gln 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/il1rn-p-asp112 (accessed [today's date]).

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