Is PAX7 p.Pro293= (c.879A>G) pathogenic?

PAX7 p.Pro293= (c.879A>G) is classified Benign in PAX7 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-26). Common (popmax 59.4%, afr) — too common for a highly-penetrant pathogenic allele; Associated with myopathy, congenital, progressive, with scoliosis.

What condition is associated with PAX7 p.Pro293= (c.879A>G)?

PAX7 p.Pro293= (c.879A>G) is associated with myopathy, congenital, progressive, with scoliosis (ClinVar).

PAX7 p.Pro293=

Q: How common is PAX7 p.Pro293= (c.879A>G) in the general population?

PAX7 p.Pro293= (c.879A>G) is common (popmax 59.4%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.879A>G · rs2743201 · VCV1326989

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 59.4%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

myopathy, congenital, progressive, with scoliosis

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 -6.5	GERP -5.4
Overall
CADD	0.248	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 59.4% African / African-American · 43,610/73,462 alleles

Filtering AF 58.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 58.7%

Overall 30% 479,029/1,594,318 alleles · common exomes 420,294/1,442,522 · genomes 58,735/151,796 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	59.4%	2
East Asian	57.9%	2
Admixed American	43.3%	2
South Asian	39.5%	3
Ashkenazi Jewishnot grpmax-eligible	39.1%	3
Amishnot grpmax-eligible	36.8%	3
Remaining individualsnot grpmax-eligible	33%	3
Finnishnot grpmax-eligible	32.4%	3
Middle Eastern	31%	3
European (non-Finnish)	25.3%	4

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: PAX7
Protein: p.Pro293=
Coding: c.879A>G
MANE Select: NM_001135254
dbSNP: rs2743201
Type: single nucleotide variant
Location: chr1:18700745 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 63.21
Residue 293: a UniProt-annotated variant site (in cmyo19); a UniProt-annotated variant site (in cmyo19; loss-of-function variant resulting in a reduced muscle stem cell pool; the protein is not detected in patient muscle)

Full PAX7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

myopathy, congenital, progressive, with scoliosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PAX7 p.Pro293Leu Uncertain significance ★ ⚠ same residue
PAX7 p.Arg74Ter Pathogenic/Likely pathogenic ★★ same condition
PAX7 p.Arg215His Uncertain significance ★★ ⚠ same condition
PAX7 p.Pro112Leu Uncertain significance ★★ ⚠ same condition
PAX7 c.86-1G>A Pathogenic ★ same condition
PAX7 p.Glu248Ter Pathogenic ★ same condition
PAX7 c.1402+91T>G Uncertain significance ★ same condition
PAX7 p.Arg247Cys 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/pax7-p-pro293 (accessed [today's date]).

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