Is IL23R p.Pro320Ser (c.958C>T) pathogenic?

IL23R p.Pro320Ser (c.958C>T) is classified Uncertain significance in IL23R (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-12). AlphaMissense: likely benign (0.0911); No allele count reported in gnomAD v4.1 (AN 1,610,388).

How common is IL23R p.Pro320Ser (c.958C>T) in the general population?

IL23R p.Pro320Ser (c.958C>T) is no allele count reported in gnomAD v4.1 (AN 1,610,388) (gnomAD).

What do computational predictors say about IL23R p.Pro320Ser (c.958C>T)?

AlphaMissense predicts likely benign (score 0.0911) — an in-silico prediction, not a clinical call.

IL23R p.Pro320Ser

c.958C>T · rs1651498332 · VCV2121384

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0911 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,610,388)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0911	likely benign
REVEL	0.046	moderately benign-leaning
SaProt	LLR -5.91	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.52	GERP 0.9
Regional constraint	o/e 0.87	unconstrained · MANE · 91 kb · p 0.00044 · regional, not allelic
Overall
CADD	5.997	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,610,388). 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: IL23R
Protein: p.Pro320Ser
Coding: c.958C>T
MANE Select: NM_144701
dbSNP: rs1651498332
Type: single nucleotide variant
Location: chr1:67236715 (GRCh38)
Gene constraint: LOEUF 0.739 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.76 · 4 PDB

Full IL23R gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IL23R p.Ala531Thr Uncertain significance ★★ ⚠ same type
IL23R p.Cys115Gly Uncertain significance ★★ ⚠ same type
IL23R p.Cys558Arg Uncertain significance ★★ ⚠ same type
IL23R p.Gln465Pro Uncertain significance ★★ ⚠ same type
IL23R p.Gln564Lys Uncertain significance ★★ ⚠ same type
IL23R p.Glu169Lys Uncertain significance ★★ ⚠ same type
IL23R p.Glu205Val Uncertain significance ★★ ⚠ same type
IL23R p.Glu269Gln Uncertain significance ★★ ⚠ same type

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/il23r-p-pro320ser (accessed [today's date]).

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