Is DNAAF3 p.Arg109= (c.327A>G) pathogenic?

DNAAF3 p.Arg109= (c.327A>G) is classified Benign/Likely benign in DNAAF3 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-04). Common (popmax 24.2%, eas) — too common for a highly-penetrant pathogenic allele; Associated with primary ciliary dyskinesia.

What condition is associated with DNAAF3 p.Arg109= (c.327A>G)?

DNAAF3 p.Arg109= (c.327A>G) is associated with primary ciliary dyskinesia (ClinVar).

How is Primary ciliary dyskinesia inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DNAAF3 p.Arg109=

Q: How common is DNAAF3 p.Arg109= (c.327A>G) in the general population?

DNAAF3 p.Arg109= (c.327A>G) is common (popmax 24.2%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.327A>G · rs3848618 · VCV257688

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Common

common (popmax 24.2%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

primary ciliary dyskinesia

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 -1.7	GERP -2.4
Overall
CADD	3.525	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 24.2% East Asian · 7,678/31,690 alleles

Filtering AF 23.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 23.6%

Overall 4.06% 50,751/1,250,556 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	24.2%	4
Admixed American	24.1%	4
South Asian	11.9%	8
Remaining individualsnot grpmax-eligible	5.68%	18
African / African-American	4.94%	20
Middle Eastern	3.91%	26
Finnishnot grpmax-eligible	3.12%	32
European (non-Finnish)	2.68%	37
Ashkenazi Jewishnot grpmax-eligible	2.18%	46

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: DNAAF3
Protein: p.Arg109=
Coding: c.327A>G
dbSNP: rs3848618
Type: single nucleotide variant
Location: chr19:55162286 (GRCh38)

Full DNAAF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

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/dnaaf3-p-arg109 (accessed [today's date]).

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