PLPBP p.Ala77=
c.231A>G · VCV3648658
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.112 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP 0.37, phastCons 1 |
| Overall | ||
| CADD | 11.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,498 alleles
Overall
6.2e-05%
1/1,611,746 alleles · very rare
exomes 1/1,459,372 · genomes 0/152,374 · 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
- PLPBP
- Protein
- p.Ala77=
- Coding
- c.231A>G
- MANE Select
- NM_007198
- Type
- single nucleotide variant
- Location
- chr8:37765734 (GRCh38)
- Gene constraint
- LOEUF 1.049 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49
- Residue 77
- a UniProt-annotated variant site (in epeo1)
Similar variants
- PLPBP c.207+1G>T Pathogenic/Likely pathogenic ★★ same type
- PLPBP c.320-2A>G Pathogenic ★★ same type
- PLPBP p.Arg241Gln Pathogenic/Likely pathogenic ★★ same type
- PLPBP p.Pro87Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- PLPBP p.Ala232= Uncertain significance ★★ same type
- PLPBP p.Arg205Trp Uncertain significance ★★ ⚠ same type
- PLPBP p.Arg250Gln Uncertain significance ★★ ⚠ same type
- PLPBP p.Arg63Cys 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/plpbp-p-ala77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown