Is DNAAF3 p.Pro471= (c.1413C>T) pathogenic?

DNAAF3 p.Pro471= (c.1413C>T) is classified Likely benign in DNAAF3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-17). Ultra-rare (popmax 0.0534%, nfe); Associated with primary ciliary dyskinesia.

What condition is associated with DNAAF3 p.Pro471= (c.1413C>T)?

DNAAF3 p.Pro471= (c.1413C>T) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAAF3 p.Pro471= (c.1413C>T) in the general population?

DNAAF3 p.Pro471= (c.1413C>T) is ultra-rare (popmax 0.0534%, nfe) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

DNAAF3 p.Pro471=

c.1413C>T · rs377325487 · VCV1205824

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0534%, nfe)

Conditions

primary ciliary dyskinesia

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 -0.5	GERP -2.7
Overall
CADD	6.446	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0534% European (non-Finnish) · 630/1,180,050 alleles

Filtering AF 0.0499% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0485%

Overall 0.0421% 679/1,614,066 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0534%	1,873
Remaining individualsnot grpmax-eligible	0.0336%	2,976
South Asian	0.0132%	7,590
African / African-American	0.00933%	10,722
Admixed American	0.00666%	15,008
Finnishnot grpmax-eligible	0.0047%	21,297
East Asian	0.00446%	22,439

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.Pro471=
Coding: c.1413C>T
MANE Select: NM_001256715
dbSNP: rs377325487
Type: single nucleotide variant
Location: chr19:55159275 (GRCh38)
Gene constraint: LOEUF 1.139 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.06

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)

Similar variants

DNAAF3 c.789+1G>C Likely pathogenic ★★ same condition
DNAAF3 p.Asn252Ser Pathogenic/Likely pathogenic ★★ same condition
DNAAF3 p.Gln301Ter Pathogenic/Likely pathogenic ★★ same condition
DNAAF3 c.789+5G>C Uncertain significance ★★ same condition
DNAAF3 c.-37G>A Uncertain significance ★★ same condition
DNAAF3 p.Ala128Thr Uncertain significance ★★ ⚠ same condition
DNAAF3 p.Ala256Gly Uncertain significance ★★ ⚠ same condition
DNAAF3 p.Ala284Asp Uncertain significance ★★ ⚠ 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/dnaaf3-p-pro471 (accessed [today's date]).

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