Is DNAAF1 p.Pro511= (c.1533G>A) pathogenic?

DNAAF1 p.Pro511= (c.1533G>A) is classified Likely benign in DNAAF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-15). Ultra-rare (popmax 0.033%, sas); Associated with primary ciliary dyskinesia.

What condition is associated with DNAAF1 p.Pro511= (c.1533G>A)?

DNAAF1 p.Pro511= (c.1533G>A) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAAF1 p.Pro511= (c.1533G>A) in the general population?

DNAAF1 p.Pro511= (c.1533G>A) is ultra-rare (popmax 0.033%, sas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

DNAAF1 p.Pro511=

c.1533G>A · rs767668207 · VCV1972273

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.033%, sas)

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 -2.9	GERP -3
Overall
CADD	0.426	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.033% South Asian · 30/90,948 alleles

Filtering AF 0.0237% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0205%

Overall 0.00366% 59/1,613,912 alleles · ultra-rare exomes 57/1,461,640 · genomes 2/152,272 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.033%	3,032
Middle Eastern	0.0165%	6,062
Remaining individualsnot grpmax-eligible	0.008%	12,501
Admixed American	0.005%	19,991
European (non-Finnish)	0.00169%	58,998

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: DNAAF1
Protein: p.Pro511=
Coding: c.1533G>A
MANE Select: NM_178452
dbSNP: rs767668207
Type: single nucleotide variant
Location: chr16:84172264 (GRCh38)
Gene constraint: LOEUF 1.135 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 61.56
Residue 511: the 'disordered' region

Full DNAAF1 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

DNAAF1 p.Pro511Leu Uncertain significance ★★ ⚠ same residue
DNAAF1 p.Arg636Ter Pathogenic ★★ same condition
DNAAF1 p.Gln260Ter Pathogenic ★★ same condition
DNAAF1 p.Gln329Ter Pathogenic/Likely pathogenic ★★ same condition
DNAAF1 p.Gln64Ter Pathogenic/Likely pathogenic ★★ same condition
DNAAF1 p.Leu232Val Likely pathogenic ★★ ⚠ same condition
DNAAF1 p.Lys626Ter Pathogenic/Likely pathogenic ★★ same condition
DNAAF1 p.Tyr264Ter 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/dnaaf1-p-pro511 (accessed [today's date]).

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