DNAH1 p.Arg3608=
c.10824G>A · VCV3589465
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
2
spermatogenic failure 18
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.36 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.33 | loss · gain 0.32 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 18.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,042 alleles
Overall
6.84e-05%
1/1,460,994 alleles · very rare
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
- DNAH1
- Protein
- p.Arg3608=
- Coding
- c.10824G>A
- MANE Select
- NM_015512
- Type
- single nucleotide variant
- Location
- chr3:52394915 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Residue 3608
- a UniProt-annotated variant site (in spgf18)
Similar variants
- DNAH1 p.Arg3608Gln Uncertain significance ★ ⚠ same residue
- DNAH1 c.1034-2A>G Likely pathogenic ★★ same condition
- DNAH1 c.10474+1G>A Pathogenic/Likely pathogenic ★★ same condition
- DNAH1 c.10968+2C>T Likely pathogenic ★★ same condition
- DNAH1 c.5244+1G>A Likely pathogenic ★★ same condition
- DNAH1 p.Arg1702Ter Pathogenic ★★ same condition
- DNAH1 p.Arg2479Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAH1 p.Arg2622Ter Pathogenic/Likely pathogenic ★★ same condition
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/dnah1-p-arg3608 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown