H6PD p.Phe62=
c.186C>T · rs116196265 · VCV777319
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.6%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 8.218 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.6%
African / African-American · 1,951/75,046 alleles
Filtering AF
2.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.46%
Overall
0.138%
2,233/1,614,200 alleles · low-frequency
exomes 1,091/1,461,878 · genomes 1,142/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.6% | 38 |
| Remaining individualsnot grpmax-eligible | 0.222% | 450 |
| Admixed American | 0.177% | 566 |
| Middle Eastern | 0.066% | 1,516 |
| South Asian | 0.00329% | 30,363 |
| European (non-Finnish) | 0.00254% | 39,334 |
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
- H6PD
- Protein
- p.Phe62=
- Coding
- c.186C>T
- MANE Select
- NM_004285
- dbSNP
- rs116196265
- Type
- single nucleotide variant
- Location
- chr1:9245120 (GRCh38)
- Gene constraint
- LOEUF 1.011 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 90.89 · 1 PDB
- Residue 62
- the 'hexose-6-phosphate dehydrogenase' region; a β-strand
Similar variants
- H6PD p.Tyr316Ter Pathogenic ★★ same type
- H6PD p.Ala286Val Uncertain significance ★★ ⚠ same type
- H6PD p.Ala299Val Uncertain significance ★★ ⚠ same type
- H6PD p.Ala338Thr Uncertain significance ★★ ⚠ same type
- H6PD p.Ala605Val Uncertain significance ★★ ⚠ same type
- H6PD p.Arg109His Uncertain significance ★★ ⚠ same type
- H6PD p.Arg250Cys Uncertain significance ★★ ⚠ same type
- H6PD p.Arg250His Uncertain significance ★★ ⚠ same type
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/h6pd-p-phe62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown