Is DHX32 p.Asp461= (c.1383C>T) pathogenic?

DHX32 p.Asp461= (c.1383C>T) is classified Likely benign in DHX32 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-19). Very rare (popmax 0.00637%, nfe).

How common is DHX32 p.Asp461= (c.1383C>T) in the general population?

DHX32 p.Asp461= (c.1383C>T) is very rare (popmax 0.00637%, nfe) (gnomAD).

DHX32 p.Asp461=

c.1383C>T · VCV3712464

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00637%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5	GERP -0.63, phastCons 1
Overall
CADD	12.22	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00637% European (non-Finnish) · 75/1,177,848 alleles

Filtering AF 0.0052% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00474%

Overall 0.00505% 81/1,605,204 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00637%	15,705
Remaining individualsnot grpmax-eligible	0.00321%	31,105
Finnishnot grpmax-eligible	0.00315%	31,791
Admixed American	0.00172%	57,976
African / African-American	0.00134%	74,452

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.Asp461=
Coding: c.1383C>T
MANE Select: NM_078468 · reported on NM_018180
Type: single nucleotide variant
Location: chr10:125841903 (GRCh38)

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

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-asp461 (accessed [today's date]).

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