Is DNAAF3 p.Val170= (c.510A>G) pathogenic?

DNAAF3 p.Val170= (c.510A>G) is classified Benign/Likely benign in DNAAF3 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-04). Common (popmax 29.1%, amr) — too common for a highly-penetrant pathogenic allele; Associated with primary ciliary dyskinesia.

What condition is associated with DNAAF3 p.Val170= (c.510A>G)?

DNAAF3 p.Val170= (c.510A>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.Val170=

Q: How common is DNAAF3 p.Val170= (c.510A>G) in the general population?

DNAAF3 p.Val170= (c.510A>G) is common (popmax 29.1%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.510A>G · rs56726774 · VCV257689

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Common

common (popmax 29.1%, amr) — 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 assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.28	GERP -0.89, phastCons 0.99
Overall
CADD	8.643	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 29.1% Admixed American · 12,647/43,480 alleles

Filtering AF 28.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 28.5%

Overall 4.79% 70,947/1,480,518 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	29.1%	3
East Asian	23.8%	4
South Asian	11.5%	9
African / African-American	6.17%	16
Remaining individualsnot grpmax-eligible	5.79%	17
Middle Eastern	4%	25
Finnishnot grpmax-eligible	3.19%	31
European (non-Finnish)	2.71%	37
Ashkenazi Jewishnot grpmax-eligible	2.16%	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.Val170=
Coding: c.510A>G
MANE Select: NM_001256715
dbSNP: rs56726774
Type: single nucleotide variant
Location: chr19:55161796 (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 p.Val170Leu Uncertain significance ★ ⚠ same residue
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

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-val170 (accessed [today's date]).

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