Is IL7R p.Phe146fs (c.437_438del) pathogenic?

IL7R p.Phe146fs (c.437438del) is classified Pathogenic/Likely pathogenic in IL7R (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-03-30). Absent from gnomAD; Associated with immunodeficiency 104.

What condition is associated with IL7R p.Phe146fs (c.437_438del)?

IL7R p.Phe146fs (c.437_438del) is associated with immunodeficiency 104, severe combined immunodeficiency (ClinVar).

How common is IL7R p.Phe146fs (c.437_438del) in the general population?

IL7R p.Phe146fs (c.437_438del) is absent from gnomAD (gnomAD).

IL7R p.Phe146fs

c.437_438del · rs1561423197 · VCV565662

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

immunodeficiency 104

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.32	GERP 1.4, phastCons 0.16

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: IL7R
Protein: p.Phe146fs
Coding: c.437_438del
MANE Select: NM_002185
dbSNP: rs1561423197
Type: Deletion
Location: chr5:35871112 (GRCh38)
Gene constraint: LOEUF 0.981 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.52 · 8 PDB
Residue 146: a β-strand; 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

Also linked: severe combined immunodeficiency

Similar variants

IL7R p.Ala76fs Pathogenic ★ same condition
IL7R p.Asn27fs Pathogenic ★ same condition
IL7R p.Cys287fs Pathogenic ★ same condition
IL7R p.Glu172fs Pathogenic ★ same condition
IL7R p.His165fs Pathogenic ★ same condition
IL7R p.Ile208fs Pathogenic ★ same condition
IL7R p.Lys120_Ile121insTer Likely pathogenic ★ same condition
IL7R p.Lys161fs 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-phe146fs (accessed [today's date]).

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