Is IL1RN p.Arg102fs (c.306_312del) pathogenic?

IL1RN p.Arg102fs (c.306312del) is classified Uncertain significance in IL1RN (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-07). No gnomAD frequency available for this variant; Associated with sterile multifocal osteomyelitis with periostitis and pustulosis.

What condition is associated with IL1RN p.Arg102fs (c.306_312del)?

IL1RN p.Arg102fs (c.306_312del) is associated with sterile multifocal osteomyelitis with periostitis and pustulosis (ClinVar).

How common is IL1RN p.Arg102fs (c.306_312del) in the general population?

IL1RN p.Arg102fs (c.306_312del) is no gnomAD frequency available for this variant (gnomAD).

IL1RN p.Arg102fs

Q: How is Sterile multifocal osteomyelitis with periostitis and pustulosis inherited?

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

c.306_312del · rs2466960959 · VCV2135127

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

sterile multifocal osteomyelitis with periostitis and pustulosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon within the last 50 nt of the penultimate exon (3 of 4, 16 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.58	GERP -2.9

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: IL1RN
Protein: p.Arg102fs
Coding: c.306_312del
MANE Select: NM_173842
dbSNP: rs2466960959
Type: Deletion
Location: chr2:113131141 (GRCh38)
Gene constraint: LOEUF 1.507 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.98 · 5 PDB
Residue 102: a β-strand

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

Disease context

sterile multifocal osteomyelitis with periostitis and pustulosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Sterile multifocal osteomyelitis with periostitis and pustulosis (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

IL1RN p.Arg102Thr Uncertain significance ★★ ⚠ same residue
IL1RN p.Asn52fs Pathogenic/Likely pathogenic ★★ same condition
IL1RN p.Asp72_Ile76del Pathogenic ★ same condition
IL1RN p.Leu16fs Likely pathogenic ★ same condition
IL1RN p.Asp129fs Uncertain significance ★ same condition
IL1RN c.206-16del Benign ★ same condition
IL1RN c.319-16_319-12del Likely benign ★ same condition
IL1RN p.Glu77Ter Pathogenic ★★ 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-arg102fs (accessed [today's date]).

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