Is IL10 p.Leu112= (c.334C>T) pathogenic?

IL10 p.Leu112= (c.334C>T) is classified Likely benign in IL10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-07-03). Absent from gnomAD v4.1; Associated with inflammatory bowel disease.

What condition is associated with IL10 p.Leu112= (c.334C>T)?

IL10 p.Leu112= (c.334C>T) is associated with inflammatory bowel disease (ClinVar).

How common is IL10 p.Leu112= (c.334C>T) in the general population?

IL10 p.Leu112= (c.334C>T) is absent from gnomAD v4.1 (gnomAD).

IL10 p.Leu112=

c.334C>T · rs2102439153 · VCV1298449

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

inflammatory bowel disease

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 3.9	GERP 1.5, phastCons 1
Overall
CADD	6.411	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: IL10
Protein: p.Leu112=
Coding: c.334C>T
MANE Select: NM_000572
dbSNP: rs2102439153
Type: single nucleotide variant
Location: chr1:206770951 (GRCh38)
Gene constraint: LOEUF 0.711 · pLI 0.48 (gnomAD)
Structure: AlphaFold pLDDT 88.89 · 9 PDB
Residue 112: an α-helix; a disulfide bond

Full IL10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

inflammatory bowel disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

IL10 c.225+6A>G Uncertain significance ★★ same condition
IL10 p.Arg124Trp Uncertain significance ★★ ⚠ same condition
IL10 p.Arg177Ter Uncertain significance ★★ same condition
IL10 p.Glu169Asp Uncertain significance ★★ ⚠ same condition
IL10 p.Leu13Met Uncertain significance ★★ ⚠ same condition
IL10 c.165+20G>A Likely benign ★★ same condition
IL10 c.165+8T>C Benign/Likely benign ★★ same condition
IL10 c.166-15T>C Benign/Likely benign ★★ 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/il10-p-leu112 (accessed [today's date]).

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