HYDIN p.Phe4902=
c.14706C>T · VCV4930754
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.075%, 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 -8.9 | GERP -3.5 |
| Overall | ||
| CADD | 0.175 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.075%
Admixed American · 45/60,006 alleles
Filtering AF
0.0576%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0514%
Overall
0.0057%
92/1,614,022 alleles · ultra-rare
exomes 87/1,461,884 · genomes 5/152,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.075% | 1,333 |
| East Asian | 0.0134% | 7,483 |
| European (non-Finnish) | 0.00339% | 29,500 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
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.Phe4902=
- Coding
- c.14706C>T
- MANE Select
- NM_001270974
- Type
- single nucleotide variant
- Location
- chr16:70809960 (GRCh38)
- Gene constraint
- LOEUF 0.555 · pLI <0.01 (gnomAD)
- Residue 4902
- a UniProt-annotated variant site (in cild5; uncertain significance); a UniProt-annotated variant site (in cild5; likely pathogenic; absence of spef2 in ciliary axonemes of respiratory cells)
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-phe4902 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown