DNHD1 p.His3022Pro
c.9065A>C · rs142389357 · VCV2390997
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0751 | likely benign |
|---|---|---|
| REVEL | 0.095 | moderately benign-leaning |
| ⇒ AlphaMissense and REVEL both call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.5 | GERP -3.4 |
| Regional constraint | o/e 0.90 | unconstrained · MANE · 66 kb · p 5.3e-11 · regional, not allelic |
| Overall | ||
| CADD | 0.212 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Amishnot grpmax-eligible | 0.768% | 130 |
| European (non-Finnish)grpmax | 0.0958% | 1,044 |
| Finnishnot grpmax-eligible | 0.0801% | 1,248 |
| Remaining individualsnot grpmax-eligible | 0.0699% | 1,431 |
| African / African-American | 0.0109% | 9,145 |
| Admixed American | 0.00392% | 25,505 |
| South Asian | 0.00119% | 84,064 |
Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- DNHD1
- Protein
- p.His3022Pro
- Coding
- c.9065A>C
- MANE Select
- NM_144666
- dbSNP
- rs142389357
- Type
- single nucleotide variant
- Location
- chr11:6558547 (GRCh38)
- Gene constraint
- LOEUF 0.897 · pLI <0.01 (gnomAD)
- Residue 3022
- a UniProt-annotated variant site (in spgf65); a UniProt-annotated variant site (in spgf65; low expression, if any, in sperm flagella)
Similar variants
- DNHD1 p.Arg2928Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Arg3978Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Arg4048Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Glu1153Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Tyr2166Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Arg1582Trp Uncertain significance ★★ same type
- DNHD1 p.Arg1873Ser Uncertain significance ★★ same type
- DNHD1 p.Arg2555Trp 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/dnhd1-p-his3022pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown