Is PAX3 p.Ser23= (c.69C>T) pathogenic?

PAX3 p.Ser23= (c.69C>T) is classified Likely benign in PAX3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-28). Very rare (popmax 0.00112%, sas).

How common is PAX3 p.Ser23= (c.69C>T) in the general population?

PAX3 p.Ser23= (c.69C>T) is very rare (popmax 0.00112%, sas) (gnomAD).

PAX3 p.Ser23=

c.69C>T · rs2469495155 · VCV2780971

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00112%, sas)

⚠ 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 3.6	GERP 0.028, phastCons 1
Overall
CADD	13.32	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00112% South Asian · 1/89,580 alleles

Overall 6.23e-05% 1/1,605,282 alleles · very rare exomes 1/1,452,916 · genomes 0/152,366 · 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: PAX3
Protein: p.Ser23=
Coding: c.69C>T
MANE Select: NM_181458
dbSNP: rs2469495155
Type: single nucleotide variant
Location: chr2:222298547 (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-ser23 (accessed [today's date]).

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