Is PCBD1 p.Leu8= (c.24G>A) pathogenic?

PCBD1 p.Leu8= (c.24G>A) is classified Likely benign in PCBD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-19). Very rare (popmax 0.000169%, nfe); Associated with pterin-4 alpha-carbinolamine dehydratase 1 deficiency.

What condition is associated with PCBD1 p.Leu8= (c.24G>A)?

PCBD1 p.Leu8= (c.24G>A) is associated with pterin-4 alpha-carbinolamine dehydratase 1 deficiency (ClinVar).

How common is PCBD1 p.Leu8= (c.24G>A) in the general population?

PCBD1 p.Leu8= (c.24G>A) is very rare (popmax 0.000169%, nfe) (gnomAD).

PCBD1 p.Leu8=

Q: How is Hyperphenylalaninemia due to tetrahydrobiopterin deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.24G>A · rs775598635 · VCV2802908

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000169%, nfe)

Conditions

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 -2	GERP -3.9
Overall
CADD	3.107	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000169% European (non-Finnish) · 2/1,179,986 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000124% 2/1,613,986 alleles · very rare exomes 2/1,461,674 · genomes 0/152,312 · 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: PCBD1
Protein: p.Leu8=
Coding: c.24G>A
MANE Select: NM_000281
dbSNP: rs775598635
Type: single nucleotide variant
Location: chr10:70885909 (GRCh38)
Gene constraint: LOEUF 1.685 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.55

Full PCBD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

pterin-4 alpha-carbinolamine dehydratase 1 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For 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-leu8 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown