Is DNAAF3 p.Thr2= (c.6C>T) pathogenic?

DNAAF3 p.Thr2= (c.6C>T) is classified Benign/Likely benign in DNAAF3 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-01). Low-frequency (popmax 1.46%, nfe); Associated with primary ciliary dyskinesia 2.

What condition is associated with DNAAF3 p.Thr2= (c.6C>T)?

DNAAF3 p.Thr2= (c.6C>T) is associated with primary ciliary dyskinesia 2, primary ciliary dyskinesia (ClinVar).

How common is DNAAF3 p.Thr2= (c.6C>T) in the general population?

DNAAF3 p.Thr2= (c.6C>T) is low-frequency (popmax 1.46%, 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.Thr2=

c.6C>T · rs150362958 · VCV238684

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.46%, nfe)

Conditions

primary ciliary dyskinesia 2

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 2	GERP 1.6, phastCons 1
Overall
CADD	12.79	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.46% European (non-Finnish) · 17,170/1,179,882 alleles

Filtering AF 1.44% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.43%

Overall 1.18% 19,062/1,613,794 alleles · low-frequency

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	1.46%	69
Remaining individualsnot grpmax-eligible	0.867%	115
Finnishnot grpmax-eligible	0.794%	126
South Asian	0.4%	250
Admixed American	0.392%	255
Middle Eastern	0.28%	357
Ashkenazi Jewishnot grpmax-eligible	0.23%	435
African / African-American	0.211%	475
East Asian	0.00223%	44,868

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.Thr2=
Coding: c.6C>T
dbSNP: rs150362958
Type: single nucleotide variant
Location: chr19:55166408 (GRCh38)

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

Disease context

primary ciliary dyskinesia 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: primary ciliary dyskinesia

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-thr2 (accessed [today's date]).

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