PGM1 p.Asp463=
c.1389C>T · rs2523935457 · VCV3058157
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
1
PGM1-related disorder
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 0.62 | GERP 0.21, phastCons 1 |
| Overall | ||
| CADD | 6.785 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,070 alleles
Overall
6.2e-05%
1/1,613,930 alleles · very rare
exomes 1/1,461,674 · genomes 0/152,256 · 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
- PGM1
- Protein
- p.Asp463=
- Coding
- c.1389C>T
- MANE Select
- NM_002633
- dbSNP
- rs2523935457
- Type
- single nucleotide variant
- Location
- chr1:63651777 (GRCh38)
- Gene constraint
- LOEUF 1.189 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 97.27 · 16 PDB
Disease context
PGM1-related disorder
Similar variants
- PGM1 p.Asp263Tyr Pathogenic/Likely pathogenic ★★ same condition
- PGM1 p.Gly291Arg Pathogenic/Likely pathogenic ★★ same condition
- PGM1 p.Gly330Arg Pathogenic/Likely pathogenic ★★ same condition
- PGM1 p.Gln324Ter Likely pathogenic ★ same condition
- PGM1 p.Ile129Thr Uncertain significance ⚠ same condition
- PGM1 c.1145-212A>G Likely benign same condition
- PGM1 c.1600-505T>C Likely benign same condition
- PGM1 c.682+5A>G Likely benign 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/pgm1-p-asp463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown