Is IL7R p.Pro329= (c.987T>A) pathogenic?

IL7R p.Pro329= (c.987T>A) is classified Likely benign in IL7R (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-06). Absent from gnomAD v4.1; Associated with immunodeficiency 104.

What condition is associated with IL7R p.Pro329= (c.987T>A)?

IL7R p.Pro329= (c.987T>A) is associated with immunodeficiency 104 (ClinVar).

How common is IL7R p.Pro329= (c.987T>A) in the general population?

IL7R p.Pro329= (c.987T>A) is absent from gnomAD v4.1 (gnomAD).

IL7R p.Pro329=

c.987T>A · rs2149905399 · VCV2716315

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 -0.085	GERP 1.9
Overall
CADD	1.225	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.Pro329=
Coding: c.987T>A
MANE Select: NM_002185
dbSNP: rs2149905399
Type: single nucleotide variant
Location: chr5:35876093 (GRCh38)
Gene constraint: LOEUF 0.981 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.52 · 8 PDB

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 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
IL7R p.Gln89Ter Likely 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-pro329 (accessed [today's date]).

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