DNHD1 p.Thr3028=
c.9084C>T · rs903169942 · VCV797503
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0499%, mid)
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 0.068 | GERP -3.7, phastCons 0.16 |
| Overall | ||
| CADD | 3.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0499%
Middle Eastern · 3/6,014 alleles
Filtering AF
0.0135%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00724%
Overall
0.00168%
26/1,551,646 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0499% | 2,005 |
| Remaining individualsnot grpmax-eligible | 0.00499% | 20,033 |
| Admixed American | 0.00392% | 25,492 |
| South Asian | 0.00357% | 28,024 |
| East Asian | 0.00244% | 40,934 |
| European (non-Finnish) | 0.00122% | 81,929 |
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.Thr3028=
- Coding
- c.9084C>T
- MANE Select
- NM_144666
- dbSNP
- rs903169942
- Type
- single nucleotide variant
- Location
- chr11:6558566 (GRCh38)
- Gene constraint
- LOEUF 0.897 · pLI <0.01 (gnomAD)
- Residue 3028
- 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-thr3028 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown