Is PAX3 p.Pro16= (c.48G>A) pathogenic?

PAX3 p.Pro16= (c.48G>A) is classified Likely benign in PAX3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-29). Very rare (popmax 0.00492%, nfe).

How common is PAX3 p.Pro16= (c.48G>A) in the general population?

PAX3 p.Pro16= (c.48G>A) is very rare (popmax 0.00492%, nfe) (gnomAD).

PAX3 p.Pro16=

c.48G>A · VCV4960178

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00492%, nfe)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.3	GERP -3.6, phastCons 0.001
Overall
CADD	10.62	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00492% European (non-Finnish) · 58/1,177,680 alleles

Filtering AF 0.00386% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00353%

Overall 0.00386% 62/1,607,832 alleles · very rare exomes 60/1,455,580 · genomes 2/152,252 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00492%	20,305
Remaining individualsnot grpmax-eligible	0.00483%	20,703
South Asian	0.00111%	90,006

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: PAX3
Protein: p.Pro16=
Coding: c.48G>A
MANE Select: NM_181458
Type: single nucleotide variant
Location: chr2:222298568 (GRCh38)

Full PAX3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/pax3-p-pro16 (accessed [today's date]).

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