HYCC1 p.Val9=
c.27G>A · rs139314533 · VCV1459851
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0241%, afr)
Conditions
1
leukodystrophy, hypomyelinating, 5
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 0.58 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 8.325 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0241%
African / African-American · 18/74,834 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0128%
Overall
0.00168%
27/1,610,118 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0241% | 4,157 |
| Admixed American | 0.00167% | 59,988 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,346 |
| South Asian | 0.0011% | 90,988 |
| European (non-Finnish) | 0.00051% | 196,127 |
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
- HYCC1
- Protein
- p.Val9=
- Coding
- c.27G>A
- MANE Select
- NM_032581
- dbSNP
- rs139314533
- Type
- single nucleotide variant
- Location
- chr7:22991085 (GRCh38)
- Structure
- AlphaFold pLDDT 68.51 · 5 PDB
- Residue 9
- an α-helix
Similar variants
- HYCC1 c.414+1G>T Pathogenic/Likely pathogenic ★★ same condition
- HYCC1 p.Gln49Ter Likely pathogenic ★★ same condition
- HYCC1 p.Leu241Ter Pathogenic/Likely pathogenic ★★ same condition
- HYCC1 c.831+5G>A Uncertain significance ★★ same condition
- HYCC1 p.Ala256Pro Uncertain significance ★★ ⚠ same condition
- HYCC1 p.Ala259Thr Uncertain significance ★★ ⚠ same condition
- HYCC1 p.Ala88Ser Uncertain significance ★★ ⚠ same condition
- HYCC1 p.Arg299Lys 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/hycc1-p-val9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown