Is DDX41 p.Arg162= (c.486C>T) pathogenic?

DDX41 p.Arg162= (c.486C>T) is classified Likely benign in DDX41 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-12-29). Ultra-rare (popmax 0.0187%, sas); Associated with Inborn genetic diseases.

What condition is associated with DDX41 p.Arg162= (c.486C>T)?

DDX41 p.Arg162= (c.486C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DDX41 p.Arg162= (c.486C>T) in the general population?

DDX41 p.Arg162= (c.486C>T) is ultra-rare (popmax 0.0187%, sas) (gnomAD).

DDX41 p.Arg162=

c.486C>T · rs762590009 · VCV2919293

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0187%, sas)

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 -11	GERP -4
Overall
CADD	0.473	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0187% South Asian · 17/91,090 alleles

Filtering AF 0.0118% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00976%

Overall 0.00266% 43/1,614,036 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0187%	5,358
African / African-American	0.004%	24,974
European (non-Finnish)	0.00178%	56,193
Admixed American	0.00167%	60,008
Remaining individualsnot grpmax-eligible	0.0016%	62,482

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.Arg162=
Coding: c.486C>T
MANE Select: NM_016222
dbSNP: rs762590009
Type: single nucleotide variant
Location: chr5:177515770 (GRCh38)
Gene constraint: LOEUF 0.768 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.38 · 5 PDB
Residue 162: 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.Arg162Gly Uncertain significance ★ ⚠ same residue
DDX41 p.Arg162His Uncertain significance ★ ⚠ same residue
DDX41 p.Arg162Cys 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

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-arg162 (accessed [today's date]).

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