DNAH3 p.Asp2467=
c.7401C>T · rs139502385 · VCV2646294
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.525%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.41 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -5.8 |
| Overall | ||
| CADD | 0.059 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.525%
European (non-Finnish) · 6,199/1,180,030 alleles
Filtering AF
0.514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.51%
Overall
0.443%
7,156/1,614,100 alleles · rare
exomes 6,695/1,461,892 · genomes 461/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.525% | 190 |
| Middle Eastern | 0.445% | 225 |
| Remaining individualsnot grpmax-eligible | 0.389% | 257 |
| South Asian | 0.363% | 275 |
| Ashkenazi Jewishnot grpmax-eligible | 0.314% | 318 |
| Admixed American | 0.227% | 441 |
| African / African-American | 0.117% | 852 |
| Finnishnot grpmax-eligible | 0.0593% | 1,685 |
| East Asian | 0.00223% | 44,876 |
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.Asp2467=
- Coding
- c.7401C>T
- MANE Select
- NM_001347886
- dbSNP
- rs139502385
- Type
- single nucleotide variant
- Location
- chr16:20985203 (GRCh38)
- Gene constraint
- LOEUF 0.834 · pLI <0.01 (gnomAD)
- Residue 2467
- 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); a UniProt-annotated variant site (found in a male with asthenoteratozoospermia; uncertain significance; severely impaired sperm motility; multiple morphological abnormalities of the sperm flagella; disorganization of flagellar components, notably inner dynein arms); the 'aaa 4' 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-asp2467 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown