DHX38 p.Ser1150=
c.3450C>T · rs140905863 · VCV1151953
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0702%, nfe)
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 -11 | GERP -3.9 |
| Overall | ||
| CADD | 2.133 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0702%
European (non-Finnish) · 828/1,179,412 alleles
Filtering AF
0.0662%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0646%
Overall
0.0583%
940/1,612,408 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0702% | 1,424 |
| Finnishnot grpmax-eligible | 0.0565% | 1,771 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,952 |
| Middle Eastern | 0.0332% | 3,016 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0237% | 4,223 |
| Admixed American | 0.0184% | 5,436 |
| African / African-American | 0.0147% | 6,811 |
| South Asian | 0.0132% | 7,571 |
| East Asian | 0.00224% | 44,726 |
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.Ser1150=
- Coding
- c.3450C>T
- MANE Select
- NM_014003
- dbSNP
- rs140905863
- Type
- single nucleotide variant
- Location
- chr16:72109483 (GRCh38)
- Gene constraint
- LOEUF 0.752 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.82 · 5 PDB
- Residue 1150
- a β-strand
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-ser1150 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown