Is PAX5 p.Pro80= (c.240T>G) pathogenic?

PAX5 p.Pro80= (c.240T>G) is classified Likely benign in PAX5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-03). Very rare (popmax 0.00891%, eas); Associated with Inborn genetic diseases.

What condition is associated with PAX5 p.Pro80= (c.240T>G)?

PAX5 p.Pro80= (c.240T>G) is associated with Inborn genetic diseases (ClinVar).

How common is PAX5 p.Pro80= (c.240T>G) in the general population?

PAX5 p.Pro80= (c.240T>G) is very rare (popmax 0.00891%, eas) (gnomAD).

PAX5 p.Pro80=

c.240T>G · VCV3885912

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00891%, eas)

Conditions

Inborn genetic diseases

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 1.3	GERP -3.1, phastCons 1
Overall
CADD	9.831	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00891% East Asian · 4/44,892 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0018%

Overall 0.000248% 4/1,614,198 alleles · very rare exomes 4/1,461,864 · genomes 0/152,334 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PAX5
Protein: p.Pro80=
Coding: c.240T>G
MANE Select: NM_016734
Type: single nucleotide variant
Location: chr9:37015167 (GRCh38)
Gene constraint: LOEUF 0.361 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 63.89 · 2 PDB
Residue 80: a DNA-binding region; a UniProt-annotated variant site (sequence variant); an α-helix

Full PAX5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PAX5 p.Pro80Arg Likely pathogenic ★ same residue
PAX5 p.Ala308Thr Uncertain significance ★★ ⚠ same condition
PAX5 p.Ala383Val Uncertain significance ★★ ⚠ same condition
PAX5 p.Ala45Ser Uncertain significance ★★ ⚠ same condition
PAX5 p.Arg122Gln Uncertain significance ★★ ⚠ same condition
PAX5 p.Arg239Cys Uncertain significance ★★ ⚠ same condition
PAX5 p.Gln233Lys Uncertain significance ★★ ⚠ same condition
PAX5 p.Gly202Asp Uncertain significance ★★ ⚠ 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/pax5-p-pro80 (accessed [today's date]).

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