PCBD1 p.Ile96=
c.288C>T · rs947677616 · VCV2177603
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 -0.5 | GERP -3.9, phastCons 0.001 |
| Overall | ||
| CADD | 9.312 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| African / African-Americangrpmax | 0.00133% | 75,046 |
| South Asian | 0.0011% | 91,006 |
| European (non-Finnish) | 8.47e-05% | 1,179,997 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- PCBD1
- Protein
- p.Ile96=
- Coding
- c.288C>T
- MANE Select
- NM_000281
- dbSNP
- rs947677616
- Type
- single nucleotide variant
- Location
- chr10:70883977 (GRCh38)
- Gene constraint
- LOEUF 1.685 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.55
- Residue 96
- 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.Ile96Val Uncertain significance ★ ⚠ same residue
- 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
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-ile96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown