DNAH3 p.Phe1786=
c.5358C>T · VCV4661002
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, 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 -4.6 | GERP -5.7 |
| Overall | ||
| CADD | 1.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,980 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.00124%
20/1,613,660 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,993 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,233 |
| European (non-Finnish) | 0.00127% | 78,660 |
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
- DNAH3
- Protein
- p.Phe1786=
- Coding
- c.5358C>T
- MANE Select
- NM_001347886
- Type
- single nucleotide variant
- Location
- chr16:21027071 (GRCh38)
- Gene constraint
- LOEUF 0.834 · pLI <0.01 (gnomAD)
- Residue 1786
- a UniProt-annotated variant site (found in a male with oligoasthenoteratozoospermia; uncertain significance; severely impaired sperm motility; multiple morphological abnormalities of the sperm flagella; partial loss and disintegration of the flagellar axoneme, accompanied by damage to the mitochondrial sheath); the 'aaa 2' region
Similar variants
- DNAH3 p.Ala1918Gly Uncertain significance ★★ ⚠ same type
- DNAH3 p.Arg1228Gln Uncertain significance ★★ same type
- DNAH3 p.Arg635Gln Uncertain significance ★★ same type
- DNAH3 p.Asn1728Ser Uncertain significance ★★ ⚠ same type
- DNAH3 p.Asp3656Asn Uncertain significance ★★ same type
- DNAH3 p.Leu2597Val Uncertain significance ★★ same type
- DNAH3 p.Leu4044Phe Uncertain significance ★★ ⚠ same type
- DNAH3 p.Lys374Gln 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/dnah3-p-phe1786 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown