Is IL10 p.Pro131= (c.393C>T) pathogenic?

IL10 p.Pro131= (c.393C>T) is classified Likely benign in IL10 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-02-20). Very rare (popmax 0.00891%, eas); Associated with inflammatory bowel disease.

What condition is associated with IL10 p.Pro131= (c.393C>T)?

IL10 p.Pro131= (c.393C>T) is associated with inflammatory bowel disease (ClinVar).

How common is IL10 p.Pro131= (c.393C>T) in the general population?

IL10 p.Pro131= (c.393C>T) is very rare (popmax 0.00891%, eas) (gnomAD).

IL10 p.Pro131=

c.393C>T · rs1229974502 · VCV1117791

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00891%, eas)

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 5.2	GERP 1.5, phastCons 1
Overall
CADD	12.78	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00891% East Asian · 4/44,896 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0018%

Overall 0.000248% 4/1,613,784 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: IL10
Protein: p.Pro131=
Coding: c.393C>T
MANE Select: NM_000572
dbSNP: rs1229974502
Type: single nucleotide variant
Location: chr1:206769880 (GRCh38)
Gene constraint: LOEUF 0.711 · pLI 0.48 (gnomAD)
Structure: AlphaFold pLDDT 88.89 · 9 PDB
Residue 131: 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-pro131 (accessed [today's date]).

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