Is DHX29 p.Ala33Pro (c.97G>C) pathogenic?

DHX29 p.Ala33Pro (c.97G>C) is classified Uncertain significance in DHX29 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-25). AlphaMissense: likely benign (0.091); Absent from gnomAD v4.1.

How common is DHX29 p.Ala33Pro (c.97G>C) in the general population?

DHX29 p.Ala33Pro (c.97G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DHX29 p.Ala33Pro (c.97G>C)?

AlphaMissense predicts likely benign (score 0.091) — an in-silico prediction, not a clinical call.

DHX29 p.Ala33Pro

c.97G>C · VCV4240195

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.091 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.091	likely benign
REVEL	0.037	moderately benign-leaning
SaProt	LLR -6.89	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 -0.15	GERP -0.21
Regional constraint	o/e 0.97	unconstrained · MANE · 22 kb · p 0.56 · regional, not allelic
Overall
CADD	8.756	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: DHX29
Protein: p.Ala33Pro
Coding: c.97G>C
MANE Select: NM_019030
Type: single nucleotide variant
Location: chr5:55307477 (GRCh38)
Gene constraint: LOEUF 0.578 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.75 · 2 PDB
Residue 33: the 'disordered' region

Full DHX29 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DHX29 p.Thr47Ala Uncertain significance ★★ ⚠ same type
DHX29 p.Ala10Pro Uncertain significance ★ ⚠ same type
DHX29 p.Ala158Thr Uncertain significance ★ ⚠ same type
DHX29 p.Ala53Thr Uncertain significance ★ ⚠ same type
DHX29 p.Arg24Thr Uncertain significance ★ ⚠ same type
DHX29 p.Arg97Ile Uncertain significance ★ ⚠ same type
DHX29 p.Asn110Ser Uncertain significance ★ ⚠ same type
DHX29 p.Asn228Thr 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/dhx29-p-ala33pro (accessed [today's date]).

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