Is IL10RA p.Pro152= (c.456C>T) pathogenic?

IL10RA p.Pro152= (c.456C>T) is classified Likely benign in IL10RA (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-26). Very rare (popmax 0.00267%, afr); Associated with inflammatory bowel disease 28.

What condition is associated with IL10RA p.Pro152= (c.456C>T)?

IL10RA p.Pro152= (c.456C>T) is associated with inflammatory bowel disease 28 (ClinVar).

How common is IL10RA p.Pro152= (c.456C>T) in the general population?

IL10RA p.Pro152= (c.456C>T) is very rare (popmax 0.00267%, afr) (gnomAD).

IL10RA p.Pro152=

Q: How is Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections syndrome inherited?

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

c.456C>T · rs376384182 · VCV2976515

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

inflammatory bowel disease 28

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 -3.1	GERP -3.5
Overall
CADD	3.121	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,884 alleles

Filtering AF 0.000954% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000787%

Overall 0.00149% 24/1,613,582 alleles · very rare exomes 20/1,461,422 · genomes 4/152,160 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,442
East Asian	0.00223%	44,902
Admixed American	0.00167%	60,000
Finnishnot grpmax-eligible	0.00156%	64,034
European (non-Finnish)	0.00153%	65,534
South Asian	0.0011%	91,070

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: IL10RA
Protein: p.Pro152=
Coding: c.456C>T
MANE Select: NM_001558
dbSNP: rs376384182
Type: single nucleotide variant
Location: chr11:117993329 (GRCh38)
Gene constraint: LOEUF 0.899 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 63.05 · 7 PDB

Full IL10RA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

inflammatory bowel disease 28 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

IL10RA p.Pro152Leu Uncertain significance ★ ⚠ same residue
IL10RA c.68-1G>A Likely pathogenic ★★ same condition
IL10RA p.Arg101Trp Pathogenic/Likely pathogenic ★★ same condition
IL10RA p.Arg117Cys Pathogenic ★★ same condition
IL10RA p.Arg165Ter Pathogenic/Likely pathogenic ★★ same condition
IL10RA p.Arg212Ter Pathogenic ★★ same condition
IL10RA p.Thr179= Pathogenic/Likely pathogenic ★★ same condition
IL10RA c.188+3G>A 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/il10ra-p-pro152 (accessed [today's date]).

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