PGK1 p.Arg18=
c.54G>C · VCV4776671
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000226%, 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 2.4 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 11.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000226%
European (non-Finnish) · 2/885,314 alleles
Filtering AF
3.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000167%
2/1,199,764 alleles · very rare
exomes 1/1,086,995 · genomes 1/112,769 · 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
- PGK1
- Protein
- p.Arg18=
- Coding
- c.54G>C
- MANE Select
- NM_000291
- Type
- single nucleotide variant
- Location
- chrX:78104394 (GRCh38)
- Structure
- AlphaFold pLDDT 96.48 · 30 PDB
- Residue 18
- a β-strand
Similar variants
- PGK1 p.Arg18Pro Uncertain significance ★ ⚠ same residue
- PGK1 p.Arg18Leu Likely benign ★ same residue
- PGK1 p.Asp164Val Pathogenic ★★ same type
- PGK1 c.116+2T>C Uncertain significance ★★ same type
- PGK1 p.Ala109Asp Uncertain significance ★★ ⚠ same type
- PGK1 p.Ala296Val Uncertain significance ★★ ⚠ same type
- PGK1 p.Ala413Thr Uncertain significance ★★ ⚠ same type
- PGK1 p.Ala55Asp Uncertain significance ★★ ⚠ 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/pgk1-p-arg18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown