Is DDX41 p.Pro238= (c.714C>T) pathogenic?

DDX41 p.Pro238= (c.714C>T) is classified Likely benign in DDX41 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-11-25). Very rare (popmax 0.00331%, nfe); Associated with Inborn genetic diseases.

What condition is associated with DDX41 p.Pro238= (c.714C>T)?

DDX41 p.Pro238= (c.714C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DDX41 p.Pro238= (c.714C>T) in the general population?

DDX41 p.Pro238= (c.714C>T) is very rare (popmax 0.00331%, nfe) (gnomAD).

DDX41 p.Pro238=

c.714C>T · rs571753440 · VCV3061657

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00331%, nfe)

Conditions

Inborn genetic diseases

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 -4.4	GERP -4.3
Overall
CADD	6.069	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00331% European (non-Finnish) · 39/1,179,876 alleles

Filtering AF 0.00247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00217%

Overall 0.0026% 42/1,613,640 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00331%	30,253
East Asian	0.00223%	44,886
Remaining individualsnot grpmax-eligible	0.0016%	62,478
South Asian	0.0011%	91,088

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: DDX41
Protein: p.Pro238=
Coding: c.714C>T
MANE Select: NM_016222
dbSNP: rs571753440
Type: single nucleotide variant
Location: chr5:177515000 (GRCh38)
Gene constraint: LOEUF 0.768 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.38 · 5 PDB
Residue 238: the helicase atp-binding domain; an α-helix

Full DDX41 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DDX41 p.Pro238Ser Uncertain significance ★★ ⚠ same residue
DDX41 p.Pro238Leu Uncertain significance ★ ⚠ same residue
DDX41 c.1303-2A>G Likely pathogenic ★★ same condition
DDX41 c.27+1G>A Likely pathogenic ★★ same condition
DDX41 c.434+1G>C Pathogenic/Likely pathogenic ★★ same condition
DDX41 c.571+1G>A Likely pathogenic ★★ same condition
DDX41 c.572-1G>A Pathogenic/Likely pathogenic ★★ same condition
DDX41 p.Arg159Ter Pathogenic ★★ 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/ddx41-p-pro238 (accessed [today's date]).

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