DNAH9 p.Pro3248=
c.9744C>T · rs12449553 · VCV1674911
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.917%, sas)
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 -14 | GERP -4.4 |
| Overall | ||
| CADD | 0.273 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.917%
South Asian · 835/91,082 alleles
Filtering AF
0.865%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.845%
Overall
0.0597%
963/1,613,982 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.917% | 109 |
| Remaining individualsnot grpmax-eligible | 0.118% | 845 |
| East Asian | 0.0446% | 2,243 |
| Middle Eastern | 0.033% | 3,031 |
| African / African-American | 0.00934% | 10,707 |
| Admixed American | 0.005% | 20,003 |
| European (non-Finnish) | 0.00186% | 53,636 |
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.Pro3248=
- Coding
- c.9744C>T
- MANE Select
- NM_001372
- dbSNP
- rs12449553
- Type
- single nucleotide variant
- Location
- chr17:11854239 (GRCh38)
- Gene constraint
- LOEUF 0.775 · pLI <0.01 (gnomAD)
- Residue 3248
- a UniProt-annotated variant site (in cild40); a UniProt-annotated variant site (in cild40; loss of localization to cilium axonema); the 'stalk' region
Similar variants
- DNAH9 p.Pro3248Leu Uncertain significance ★ same residue
- 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
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-pro3248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown