Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 45.6%, eas) — too common for a highly-penetrant pathogenic allele
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 -1.7 | GERP -8.7 |
| Overall | ||
| CADD | 0.309 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
45.6%
East Asian · 19,615/43,034 alleles
Filtering AF
45%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 44.8%
Overall
27.8%
440,499/1,584,486 alleles · common
exomes 397,009/1,435,208 · genomes 43,490/149,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 45.6% | 2 |
| Admixed American | 45.1% | 2 |
| South Asian | 33% | 3 |
| Middle Eastern | 32.1% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 31.7% | 3 |
| African / African-American | 29.5% | 3 |
| Remaining individualsnot grpmax-eligible | 29.4% | 3 |
| European (non-Finnish) | 25.9% | 4 |
| Amishnot grpmax-eligible | 23% | 4 |
| Finnishnot grpmax-eligible | 23% | 4 |
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
- HYDIN
- Protein
- p.Asp359=
- Coding
- c.1077T>C
- MANE Select
- NM_001270974
- dbSNP
- rs4788770
- Type
- single nucleotide variant
- Location
- chr16:71129790 (GRCh38)
- Gene constraint
- LOEUF 0.555 · pLI <0.01 (gnomAD)
- Residue 359
- a UniProt-annotated variant site (in cild5; uncertain significance)
Similar variants
- HYDIN c.12444-1G>A Likely pathogenic ★★ same type
- HYDIN c.12444-3C>G Likely pathogenic ★★ same type
- HYDIN c.6669+1G>A Likely pathogenic ★★ same type
- HYDIN p.Arg2120Ter Likely pathogenic ★★ same type
- HYDIN p.Arg444Ter Pathogenic/Likely pathogenic ★★ same type
- HYDIN p.Glu683Ter Pathogenic/Likely pathogenic ★★ same type
- HYDIN p.Tyr599Ter Pathogenic/Likely pathogenic ★★ same type
- HYDIN p.Arg163Gln 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/hydin-p-asp359 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown