DHX38 p.Cys1072=
c.3216C>T · rs764530124 · VCV1123239
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.035%, amr)
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 -0.016 | GERP -4.5, phastCons 0.89 |
| Overall | ||
| CADD | 6.937 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.035%
Admixed American · 21/59,998 alleles
Filtering AF
0.0234%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.00143%
23/1,614,022 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.035% | 2,857 |
| European (non-Finnish) | 0.000169% | 590,009 |
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
- DHX38
- Protein
- p.Cys1072=
- Coding
- c.3216C>T
- MANE Select
- NM_014003
- dbSNP
- rs764530124
- Type
- single nucleotide variant
- Location
- chr16:72108568 (GRCh38)
- Gene constraint
- LOEUF 0.752 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.82 · 5 PDB
- Residue 1072
- an α-helix
Similar variants
- DHX38 c.2011-3C>A Uncertain significance ★★ same type
- DHX38 c.2262+3G>C Uncertain significance ★★ same type
- DHX38 c.2262+4C>T Uncertain significance ★★ same type
- DHX38 c.2262+5G>A Uncertain significance ★★ same type
- DHX38 c.2964+3G>C Uncertain significance ★★ same type
- DHX38 c.616+3A>G Uncertain significance ★★ same type
- DHX38 c.764+2T>G Uncertain significance ★★ same type
- DHX38 p.Ala113Val 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/dhx38-p-cys1072 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown