DNAH9 p.Ala1406=
c.4218G>A · rs140079277 · VCV1619983
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.01%, afr)
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 -3.2 | GERP -5.9 |
| Overall | ||
| CADD | 0.602 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.01%
African / African-American · 760/75,050 alleles
Filtering AF
0.953%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.929%
Overall
0.0607%
979/1,614,154 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.01% | 99 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| Admixed American | 0.0583% | 1,715 |
| Middle Eastern | 0.0495% | 2,020 |
| South Asian | 0.011% | 9,108 |
| European (non-Finnish) | 0.0104% | 9,594 |
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.Ala1406=
- Coding
- c.4218G>A
- MANE Select
- NM_001372
- dbSNP
- rs140079277
- Type
- single nucleotide variant
- Location
- chr17:11690040 (GRCh38)
- Gene constraint
- LOEUF 0.775 · pLI <0.01 (gnomAD)
- Residue 1406
- the 'stem' region; a UniProt-annotated variant site (in cild40)
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-ala1406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown