PAX7 p.Pro306=
c.918G>A · rs374991984 · VCV2638405
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0583%, sas)
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 -0.18 | GERP -4.6, phastCons 0.046 |
| Overall | ||
| CADD | 12.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0583%
South Asian · 50/85,836 alleles
Filtering AF
0.0454%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0408%
Overall
0.00896%
141/1,573,466 alleles · ultra-rare
exomes 128/1,421,306 · genomes 13/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0583% | 1,717 |
| Remaining individualsnot grpmax-eligible | 0.0247% | 4,055 |
| Admixed American | 0.0218% | 4,589 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00711% | 14,065 |
| European (non-Finnish) | 0.005% | 20,004 |
| Finnishnot grpmax-eligible | 0.00317% | 31,549 |
| East Asian | 0.00246% | 40,696 |
| African / African-American | 0.00137% | 72,730 |
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.Pro306=
- Coding
- c.918G>A
- MANE Select
- NM_001135254
- dbSNP
- rs374991984
- Type
- single nucleotide variant
- Location
- chr1:18700784 (GRCh38)
- Gene constraint
- LOEUF 0.504 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 306
- 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)
Similar variants
- PAX7 p.Arg74Ter Pathogenic/Likely pathogenic ★★ same type
- PAX7 c.587-8G>A Uncertain significance ★★ same type
- PAX7 p.Ala235Thr Uncertain significance ★★ ⚠ same type
- PAX7 p.Arg215His Uncertain significance ★★ ⚠ same type
- PAX7 p.Glu201Gly Uncertain significance ★★ same type
- PAX7 p.Pro112Leu Uncertain significance ★★ ⚠ same type
- PAX7 c.1155+9T>C Benign ★★ same type
- PAX7 p.Ala259= Benign ★★ same type
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-pro306 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown