Is DHX30 p.Pro607= (c.1821C>T) pathogenic?

DHX30 p.Pro607= (c.1821C>T) is classified Likely benign in DHX30 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-15). Ultra-rare (popmax 0.05%, amr); Associated with DHX30-related disorder.

What condition is associated with DHX30 p.Pro607= (c.1821C>T)?

DHX30 p.Pro607= (c.1821C>T) is associated with DHX30-related disorder (ClinVar).

How common is DHX30 p.Pro607= (c.1821C>T) in the general population?

DHX30 p.Pro607= (c.1821C>T) is ultra-rare (popmax 0.05%, amr) (gnomAD).

DHX30 p.Pro607=

c.1821C>T · rs760943698 · VCV3050368

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.05%, amr)

Conditions

DHX30-related disorder

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 -7.1	GERP -4
Overall
CADD	1.355	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.05% Admixed American · 30/59,990 alleles

Filtering AF 0.0359% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0312%

Overall 0.00657% 106/1,613,096 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.05%	2,000
Middle Eastern	0.0164%	6,084
Remaining individualsnot grpmax-eligible	0.0112%	8,925
East Asian	0.00668%	14,962
European (non-Finnish)	0.00542%	18,437
African / African-American	0.00133%	74,916

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: DHX30
Protein: p.Pro607=
Coding: c.1821C>T
MANE Select: NM_138615
dbSNP: rs760943698
Type: single nucleotide variant
Location: chr3:47846893 (GRCh38)
Gene constraint: LOEUF 0.08 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 81.09 · 1 PDB
Residue 607: the helicase atp-binding domain

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

Disease context

DHX30-related disorder

Similar variants

DHX30 p.Arg782Trp Pathogenic ★★ same condition
DHX30 p.Gly460Asp Likely pathogenic ★ same condition
DHX30 p.Thr739Ile Likely pathogenic ★ same condition
DHX30 p.Ser225Cys Uncertain significance ★ ⚠ same condition
DHX30 p.Thr593Ile Uncertain significance ⚠ same condition
DHX30 p.Arg894= Likely benign same condition
DHX30 p.His695= Likely benign same condition
DHX30 p.Lys714= Likely benign same condition

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-pro607 (accessed [today's date]).

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