Is IL7R p.Pro132= (c.396T>A) pathogenic?

IL7R p.Pro132= (c.396T>A) is classified Likely benign in IL7R (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-17). Absent from gnomAD v4.1; Associated with immunodeficiency 104.

What condition is associated with IL7R p.Pro132= (c.396T>A)?

IL7R p.Pro132= (c.396T>A) is associated with immunodeficiency 104 (ClinVar).

How common is IL7R p.Pro132= (c.396T>A) in the general population?

IL7R p.Pro132= (c.396T>A) is absent from gnomAD v4.1 (gnomAD).

IL7R p.Pro132=

c.396T>A · VCV3641543

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

immunodeficiency 104

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 0.4	GERP 1.8, phastCons 1
Overall
CADD	5.953	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: IL7R
Protein: p.Pro132=
Coding: c.396T>A
MANE Select: NM_002185
Type: single nucleotide variant
Location: chr5:35871072 (GRCh38)
Gene constraint: LOEUF 0.981 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.52 · 8 PDB
Residue 132: a UniProt-annotated variant site (in imd104); an α-helix; the fibronectin type-iii domain

Full IL7R gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency 104 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

IL7R p.Pro132Ser Likely pathogenic ★★★ same residue
IL7R c.221+1G>A Pathogenic ★★★ same condition
IL7R c.221+2T>G Pathogenic ★★★ same condition
IL7R c.537+1G>A Pathogenic ★★★ same condition
IL7R c.538-1G>A Pathogenic ★★★ same condition
IL7R c.83-2A>T Pathogenic ★★★ same condition
IL7R p.Arg206Ter Pathogenic ★★★ same condition
IL7R p.Cys118Tyr 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/il7r-p-pro132 (accessed [today's date]).

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