SYN1 p.Pro544=
c.1632A>G · VCV4684516
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000123%, nfe)
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 0.4 | phastCons 0.69 |
| Overall | ||
| CADD | 8.706 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000123%
European (non-Finnish) · 1/814,196 alleles
Overall
9.68e-05%
1/1,033,278 alleles · very rare
exomes 1/922,024 · genomes 0/111,254 · 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
- SYN1
- Protein
- p.Pro544=
- Coding
- c.1632A>G
- MANE Select
- NM_006950
- Type
- single nucleotide variant
- Location
- chrX:47574352 (GRCh38)
- Structure
- AlphaFold pLDDT 69.86
- Residue 544
- the 'disordered' region; the 'd; pro-rich linker' region
Similar variants
- SYN1 c.528-2A>T Pathogenic/Likely pathogenic ★★ same type
- SYN1 c.838-2A>G Likely pathogenic ★★ same type
- SYN1 p.Arg234Ter Pathogenic ★★ same type
- SYN1 p.Arg420Gln Likely pathogenic ★★ ⚠ same type
- SYN1 p.Arg422Ter Pathogenic ★★ same type
- SYN1 p.Gln249Ter Pathogenic/Likely pathogenic ★★ same type
- SYN1 p.Gln483Ter Pathogenic ★★ same type
- SYN1 p.Gln555Ter Pathogenic ★★ 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/syn1-p-pro544 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown