GCH1 p.Val162=
c.486C>A · rs768067517 · VCV2939455
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
2
GTP cyclohydrolase I 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 0.94 | GERP 0.69, phastCons 1 |
| Overall | ||
| CADD | 6.596 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,830 alleles
Overall
0.000657%
1/152,178 alleles · very rare
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
- GCH1
- Protein
- p.Val162=
- Coding
- c.486C>A
- MANE Select
- NM_000161
- dbSNP
- rs768067517
- Type
- single nucleotide variant
- Location
- chr14:54859704 (GRCh38)
- Gene constraint
- LOEUF 0.899 · pLI 0.36 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 86.89 · 11 PDB
- Residue 162
- a β-strand
Similar variants
- GCH1 c.344-1G>A Pathogenic ★★ same condition
- GCH1 c.510-1G>A Pathogenic/Likely pathogenic ★★ same condition
- GCH1 c.541+1G>T Pathogenic ★★ same condition
- GCH1 c.541+2T>C Pathogenic ★★ same condition
- GCH1 c.626+1G>A Pathogenic/Likely pathogenic ★★ same condition
- GCH1 c.626+1G>T Pathogenic ★★ same condition
- GCH1 c.-22C>T Pathogenic/Likely pathogenic ★★ same condition
- GCH1 p.Arg184Cys 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/gch1-p-val162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown