DNHD1 p.Ala441=
c.1323C>T · rs149380422 · VCV719539
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.4%, 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 0.074 | GERP -1.8, phastCons 0.88 |
| Overall | ||
| CADD | 9.454 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.4%
African / African-American · 1,049/75,052 alleles
Filtering AF
1.33%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.3%
Overall
0.0725%
1,171/1,614,220 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.4% | 72 |
| Remaining individualsnot grpmax-eligible | 0.101% | 992 |
| Admixed American | 0.06% | 1,667 |
| Middle Eastern | 0.033% | 3,031 |
| East Asian | 0.0111% | 8,976 |
| South Asian | 0.00439% | 22,772 |
| European (non-Finnish) | 0.00102% | 98,337 |
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
- DNHD1
- Protein
- p.Ala441=
- Coding
- c.1323C>T
- MANE Select
- NM_144666
- dbSNP
- rs149380422
- Type
- single nucleotide variant
- Location
- chr11:6511360 (GRCh38)
- Gene constraint
- LOEUF 0.897 · pLI <0.01 (gnomAD)
Similar variants
- DNHD1 p.Arg2928Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Arg3978Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Arg4048Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Glu1153Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Tyr2166Ter Pathogenic/Likely pathogenic ★★ same type
- DNHD1 p.Arg1582Trp Uncertain significance ★★ same type
- DNHD1 p.Arg1873Ser Uncertain significance ★★ same type
- DNHD1 p.Arg2555Trp 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/dnhd1-p-ala441 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown