DNAH9 p.Ser3629=
c.10887C>T · rs61742982 · VCV1294664
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 8.59%, afr) — too common for a highly-penetrant pathogenic allele
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 · C>A here scores Δ0.47 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -3.7 |
| Overall | ||
| CADD | 0.046 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.59%
African / African-American · 6,444/74,990 alleles
Filtering AF
8.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.35%
Overall
1.02%
16,413/1,614,064 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.59% | 12 |
| East Asian | 3.67% | 27 |
| Middle Eastern | 1.47% | 68 |
| Remaining individualsnot grpmax-eligible | 1.26% | 79 |
| South Asian | 1.22% | 82 |
| Admixed American | 1.04% | 96 |
| European (non-Finnish) | 0.461% | 217 |
| Ashkenazi Jewishnot grpmax-eligible | 0.321% | 312 |
| Finnishnot grpmax-eligible | 0.258% | 388 |
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
- DNAH9
- Protein
- p.Ser3629=
- Coding
- c.10887C>T
- MANE Select
- NM_001372
- dbSNP
- rs61742982
- Type
- single nucleotide variant
- Location
- chr17:11883666 (GRCh38)
- Gene constraint
- LOEUF 0.775 · pLI <0.01 (gnomAD)
- Residue 3629
- a UniProt-annotated variant site (in cild40); a UniProt-annotated variant site (in cild40; loss of localization to cilium axonema); the 'aaa 5' region
Similar variants
- DNAH9 c.11406+1G>T Likely pathogenic ★★ same type
- DNAH9 c.1901+1G>A Likely pathogenic ★★ same type
- DNAH9 c.2928+1G>A Likely pathogenic ★★ same type
- DNAH9 c.5709+1G>T Likely pathogenic ★★ same type
- DNAH9 c.615-2A>G Likely pathogenic ★★ same type
- DNAH9 c.6847+1G>A Likely pathogenic ★★ same type
- DNAH9 p.Arg1344Ter Pathogenic/Likely pathogenic ★★ same type
- DNAH9 p.Arg1517Ter Pathogenic/Likely pathogenic ★★ 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/dnah9-p-ser3629 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown