PCCB p.Phe102=
c.306T>C · rs770601332 · VCV1607990
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
propionic acidemia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.716 | pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP 0.94, phastCons 1 |
| Overall | ||
| CADD | 14.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PCCB
- Protein
- p.Phe102=
- Coding
- c.306T>C
- MANE Select
- NM_000532
- dbSNP
- rs770601332
- Type
- single nucleotide variant
- Location
- chr3:136256557 (GRCh38)
- Gene constraint
- LOEUF 0.843 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.59 · 24 PDB
- Residue 102
- the coa carboxyltransferase n-terminal domain; the 'carboxyltransferase' region
Disease context
propionic acidemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Propionic acidemia (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- >1 / 1000 (Canada)
Similar variants
- PCCB p.Phe102Cys Uncertain significance ★ ⚠ same residue
- PCCB p.Phe102Leu Uncertain significance ★ ⚠ same residue
- PCCB c.1199-1G>A Pathogenic/Likely pathogenic ★★ same condition
- PCCB c.1199-2A>G Pathogenic ★★ same condition
- PCCB c.1398+1G>C Pathogenic/Likely pathogenic ★★ same condition
- PCCB c.1398+1G>T Pathogenic/Likely pathogenic ★★ same condition
- PCCB c.1498+2T>C Pathogenic ★★ same condition
- PCCB c.1499-1G>C Pathogenic/Likely pathogenic ★★ 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/pccb-p-phe102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown