HYDIN p.Pro2185=
c.6555G>A · VCV4930917
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0168%, amr)
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 -11 | GERP -3.2 |
| Overall | ||
| CADD | 0.424 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0168%
Admixed American · 10/59,676 alleles
Filtering AF
0.00904%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00685%
Overall
0.0018%
29/1,611,410 alleles · ultra-rare
exomes 29/1,459,296 · genomes 0/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0168% | 5,968 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,802 |
| East Asian | 0.00223% | 44,790 |
| South Asian | 0.00221% | 45,252 |
| European (non-Finnish) | 0.0011% | 90,700 |
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.Pro2185=
- Coding
- c.6555G>A
- MANE Select
- NM_001270974
- Type
- single nucleotide variant
- Location
- chr16:70943926 (GRCh38)
- Gene constraint
- LOEUF 0.555 · pLI <0.01 (gnomAD)
- Residue 2185
- a UniProt-annotated variant site (in cild5; uncertain significance); the 'disordered' region; a UniProt-annotated variant site (in cild5; likely pathogenic; absence of spef2 in ciliary axonemes of respiratory cells)
Similar variants
- HYDIN p.Pro2185Leu Likely benign ★ same residue
- 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
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-pro2185 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown