DHX16 p.Ala332=
c.996G>A · rs141508885 · VCV2656338
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.243%, 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 0.77 | phastCons 1 |
| Overall | ||
| CADD | 6.675 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.243%
African / African-American · 182/75,002 alleles
Filtering AF
0.214%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.203%
Overall
0.0389%
627/1,609,766 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.243% | 412 |
| Admixed American | 0.127% | 789 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,313 |
| European (non-Finnish) | 0.0285% | 3,511 |
| Middle Eastern | 0.0165% | 6,060 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,785 |
| Finnishnot grpmax-eligible | 0.00499% | 20,059 |
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
- DHX16
- Protein
- p.Ala332=
- Coding
- c.996G>A
- MANE Select
- NM_003587
- dbSNP
- rs141508885
- Type
- single nucleotide variant
- Location
- chr6:30665200 (GRCh38)
- Gene constraint
- LOEUF 0.716 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.82 · 12 PDB
- Residue 332
- an α-helix
Similar variants
- DHX16 p.Thr674Met Pathogenic/Likely pathogenic ★★ same type
- DHX16 p.Arg940Cys Uncertain significance ★★ ⚠ same type
- DHX16 p.Arg956Gln Uncertain significance ★★ ⚠ same type
- DHX16 p.Asp580Gly Uncertain significance ★★ ⚠ same type
- DHX16 p.Glu105Lys Uncertain significance ★★ ⚠ same type
- DHX16 p.Glu995Gly Uncertain significance ★★ ⚠ same type
- DHX16 c.207+8C>G Benign/Likely benign ★★ same type
- DHX16 p.Val962= Benign ★★ 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/dhx16-p-ala332 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown