Is DNAAF2 p.Asp489= (c.1467T>C) pathogenic?

DNAAF2 p.Asp489= (c.1467T>C) is classified Likely benign in DNAAF2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-06). Ultra-rare (popmax 0.0891%, sas); Associated with primary ciliary dyskinesia.

What condition is associated with DNAAF2 p.Asp489= (c.1467T>C)?

DNAAF2 p.Asp489= (c.1467T>C) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAAF2 p.Asp489= (c.1467T>C) in the general population?

DNAAF2 p.Asp489= (c.1467T>C) is ultra-rare (popmax 0.0891%, sas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

DNAAF2 p.Asp489=

c.1467T>C · rs201056459 · VCV525529

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0891%, sas)

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Overall
CADD	2.142	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0891% South Asian · 81/90,922 alleles

Filtering AF 0.0734% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0676%

Overall 0.00653% 105/1,607,164 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0891%	1,122
East Asian	0.0201%	4,966
Remaining individualsnot grpmax-eligible	0.00805%	12,427
African / African-American	0.00134%	74,696
European (non-Finnish)	0.000766%	130,618

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: DNAAF2
Protein: p.Asp489=
Coding: c.1467T>C
MANE Select: NM_018139
dbSNP: rs201056459
Type: single nucleotide variant
Location: chr14:49633683 (GRCh38)
Gene constraint: LOEUF 1.811 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.57
Residue 489: the 'disordered' region

Full DNAAF2 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

DNAAF2 p.Asp489His Uncertain significance ★★ ⚠ same residue
DNAAF2 p.Gln504Ter Pathogenic/Likely pathogenic ★★ same condition
DNAAF2 p.Gln529Ter Pathogenic/Likely pathogenic ★★ same condition
DNAAF2 p.Glu130Ter Pathogenic/Likely pathogenic ★★ same condition
DNAAF2 p.Glu243Ter Likely pathogenic ★★ same condition
DNAAF2 p.Ala100Gly Uncertain significance ★★ ⚠ same condition
DNAAF2 p.Ala126Val Uncertain significance ★★ ⚠ same condition
DNAAF2 p.Ala211Thr 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/dnaaf2-p-asp489 (accessed [today's date]).

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