Is DHX9 p.Ala802Thr (c.2404G>A) pathogenic?

DHX9 p.Ala802Thr (c.2404G>A) is classified Uncertain significance in DHX9 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-03). AlphaMissense: likely pathogenic (0.7748); Absent from gnomAD v4.1.

How common is DHX9 p.Ala802Thr (c.2404G>A) in the general population?

DHX9 p.Ala802Thr (c.2404G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DHX9 p.Ala802Thr (c.2404G>A)?

AlphaMissense predicts likely pathogenic (score 0.7748) — an in-silico prediction, not a clinical call.

DHX9 p.Ala802Thr

c.2404G>A · VCV3897329

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7748 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,542,928)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.7748	likely pathogenic
REVEL	0.306	indeterminate
SaProt	LLR -9.19	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 1.6, phastCons 1
Regional constraint	o/e 0.42	unconstrained · MANE · 5,101 bp · p 8e-23 · regional, not allelic
Overall
CADD	25.5	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,542,928). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DHX9
Protein: p.Ala802Thr
Coding: c.2404G>A
MANE Select: NM_001357
Type: single nucleotide variant
Location: chr1:182879302 (GRCh38)
Gene constraint: LOEUF 0.263 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 81.84 · 7 PDB
Residue 802: the 'necessary for interaction with h2ax' region; the 'core helicase' region; an α-helix; the helicase c-terminal domain; a UniProt-annotated variant site (in mrd75; likely pathogenic)

Full DHX9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DHX9 p.Ala355Thr Uncertain significance ★★ ⚠ same type
DHX9 p.Asn1133His Uncertain significance ★★ ⚠ same type
DHX9 p.Pro586Ala Uncertain significance ★★ ⚠ same type
DHX9 c.364+6G>T Benign ★★ same type
DHX9 p.Ile903= Benign ★★ same type
DHX9 p.Leu244= Benign ★★ same type
DHX9 p.Tyr875= Benign ★★ same type
DHX9 c.1141-1G>A Likely pathogenic ★ 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/dhx9-p-ala802thr (accessed [today's date]).

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