Is DHX30 p.Val808Glu (c.2423T>A) pathogenic?

DHX30 p.Val808Glu (c.2423T>A) is classified Uncertain significance in DHX30 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-17). AlphaMissense: likely benign (0.3377); Absent from gnomAD v4.1.

How common is DHX30 p.Val808Glu (c.2423T>A) in the general population?

DHX30 p.Val808Glu (c.2423T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DHX30 p.Val808Glu (c.2423T>A)?

AlphaMissense predicts likely benign (score 0.3377) — an in-silico prediction, not a clinical call.

DHX30 p.Val808Glu

c.2423T>A · rs2549297240 · VCV2579793

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3377 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3377	likely benign
REVEL	0.239	benign-leaning
SaProt	LLR -7.08	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 2.3, phastCons 1
Regional constraint	o/e 0.00	constrained · MANE · 39 bp · p 6e-05 · regional, not allelic
Overall
CADD	25.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DHX30
Protein: p.Val808Glu
Coding: c.2423T>A
MANE Select: NM_138615
dbSNP: rs2549297240
Type: single nucleotide variant
Location: chr3:47848316 (GRCh38)
Gene constraint: LOEUF 0.08 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 81.09 · 1 PDB
Residue 808: the helicase c-terminal domain

Full DHX30 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DHX30 p.Arg782Gln Pathogenic/Likely pathogenic ★★ same type
DHX30 p.Arg782Trp Pathogenic ★★ same type
DHX30 p.Arg785Cys Pathogenic/Likely pathogenic ★★ same type
DHX30 p.Arg785His Pathogenic/Likely pathogenic ★★ same type
DHX30 c.2575+5G>A Uncertain significance ★★ same type
DHX30 p.Arg1180Gln Uncertain significance ★★ ⚠ same type
DHX30 p.Arg412Cys Uncertain significance ★★ ⚠ same type
DHX30 p.Arg586Gly 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/dhx30-p-val808glu (accessed [today's date]).

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