Is DHX32 p.Ala280= (c.840C>T) pathogenic?

DHX32 p.Ala280= (c.840C>T) is classified Likely benign in DHX32 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-26). Very rare (popmax 0.00117%, sas).

How common is DHX32 p.Ala280= (c.840C>T) in the general population?

DHX32 p.Ala280= (c.840C>T) is very rare (popmax 0.00117%, sas) (gnomAD).

DHX32 p.Ala280=

c.840C>T · rs2494435779 · VCV2726588

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00117%, sas)

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 4.4	GERP 0.56, phastCons 1
Overall
CADD	11.03	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00117% South Asian · 1/85,240 alleles

Overall 6.98e-05% 1/1,431,996 alleles · very rare

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: DHX32
Protein: p.Ala280=
Coding: c.840C>T
MANE Select: NM_018180
dbSNP: rs2494435779
Type: single nucleotide variant
Location: chr10:125859612 (GRCh38)
Gene constraint: LOEUF 0.919 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.34

Full DHX32 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DHX32 p.Ala251Val Uncertain significance ★★ ⚠ same type
DHX32 p.Ala93Thr Uncertain significance ★★ ⚠ same type
DHX32 p.Arg129Gln Uncertain significance ★★ ⚠ same type
DHX32 p.Arg261Cys Uncertain significance ★★ ⚠ same type
DHX32 p.Arg261His Uncertain significance ★★ ⚠ same type
DHX32 p.Asn239Lys Uncertain significance ★★ ⚠ same type
DHX32 p.Asn297His Uncertain significance ★★ ⚠ same type
DHX32 p.Asn297Ile 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/dhx32-p-ala280 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown