Is PAX2 p.Phe10fs (c.27dup) pathogenic?

PAX2 p.Phe10fs (c.27dup) is classified Likely pathogenic in PAX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-06). Associated with focal segmental glomerulosclerosis 7.

What condition is associated with PAX2 p.Phe10fs (c.27dup)?

PAX2 p.Phe10fs (c.27dup) is associated with focal segmental glomerulosclerosis 7 (ClinVar).

PAX2 p.Phe10fs

c.27dup · VCV4856418

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

focal segmental glomerulosclerosis 7

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 1 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.1	GERP 2.2, phastCons 1

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

Variant & gene context

Gene: PAX2
Protein: p.Phe10fs
Coding: c.27dup
MANE Select: NM_000278
Type: Duplication
Location: chr10:100746283 (GRCh38)
Gene constraint: LOEUF 0.451 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 61.52

Full PAX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

focal segmental glomerulosclerosis 7 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PAX2 p.Glu74_Thr75dup Pathogenic/Likely pathogenic ★★ same condition
PAX2 p.Ala120fs Likely pathogenic ★ same condition
PAX2 p.His321fs Likely pathogenic ★ same condition
PAX2 p.Ile83delinsArgValTer Pathogenic ★ same condition
PAX2 p.Ser77fs Pathogenic ★ same condition
PAX2 p.Val244fs Likely pathogenic ★ same condition
PAX2 c.411-14_411-10dup Conflicting classifications of pathogenicity ★ same condition
PAX2 c.44-12_44-8dup Conflicting classifications of pathogenicity ★ 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/pax2-p-phe10fs (accessed [today's date]).

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