PCBD1 p.Ile90=
c.270A>C · rs1413245787 · VCV3022206
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
pterin-4 alpha-carbinolamine dehydratase 1 deficiency
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 1.4 | GERP 0.93, phastCons 1 |
| Overall | ||
| CADD | 12.03 | 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
- PCBD1
- Protein
- p.Ile90=
- Coding
- c.270A>C
- MANE Select
- NM_000281
- dbSNP
- rs1413245787
- Type
- single nucleotide variant
- Location
- chr10:70883995 (GRCh38)
- Gene constraint
- LOEUF 1.685 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.55
- Residue 90
- a UniProt-annotated variant site (in hpabh4d; reduced protein levels; loss of hnf1b interaction; loss of hnf1b-coactivator activity); a UniProt-annotated variant site (in hpabh4d; increased proteolytic degradation; loss of hnf1b interaction; loss of hnf1b-coactivator activity)
Disease context
pterin-4 alpha-carbinolamine dehydratase 1 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hyperphenylalaninemia due to tetrahydrobiopterin deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Japan)
Similar variants
- PCBD1 p.Gln98Ter Pathogenic/Likely pathogenic ★★ same condition
- PCBD1 p.Glu87Ter Pathogenic/Likely pathogenic ★★ same condition
- PCBD1 p.Glu97Lys Pathogenic/Likely pathogenic ★★ same condition
- PCBD1 p.Arg13Trp Uncertain significance ★★ ⚠ same condition
- PCBD1 p.Arg31Cys Uncertain significance ★★ ⚠ same condition
- PCBD1 p.Arg88Trp Uncertain significance ★★ ⚠ same condition
- PCBD1 p.Asp61Tyr Uncertain significance ★★ ⚠ same condition
- PCBD1 p.Gln15His Uncertain significance ★★ ⚠ 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/pcbd1-p-ile90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown