Is PAX5 p.Pro258= (c.774C>T) pathogenic?

PAX5 p.Pro258= (c.774C>T) is classified Likely benign in PAX5 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-02-10). Very rare (popmax 0.00754%, nfe); Associated with Inborn genetic diseases.

What condition is associated with PAX5 p.Pro258= (c.774C>T)?

PAX5 p.Pro258= (c.774C>T) is associated with Inborn genetic diseases (ClinVar).

How common is PAX5 p.Pro258= (c.774C>T) in the general population?

PAX5 p.Pro258= (c.774C>T) is very rare (popmax 0.00754%, nfe) (gnomAD).

PAX5 p.Pro258=

c.774C>T · rs113556063 · VCV1337574

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00754%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -15	GERP -5.6
Overall
CADD	0.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00754% European (non-Finnish) · 89/1,179,598 alleles

Filtering AF 0.00623% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00579%

Overall 0.00583% 94/1,613,562 alleles · very rare exomes 89/1,461,222 · genomes 5/152,340 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00754%	13,254
East Asian	0.00669%	14,953
Remaining individualsnot grpmax-eligible	0.0016%	62,476
African / African-American	0.00133%	75,062

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.Pro258=
Coding: c.774C>T
MANE Select: NM_016734
dbSNP: rs113556063
Type: single nucleotide variant
Location: chr9:36966555 (GRCh38)
Gene constraint: LOEUF 0.361 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 63.89 · 2 PDB

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.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
PAX5 p.Ile114Val 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-pro258 (accessed [today's date]).

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