Is DNAL1 p.Ala166= (c.498A>T) pathogenic?

DNAL1 p.Ala166= (c.498A>T) is classified Likely benign in DNAL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-20). Ultra-rare (popmax 0.0433%, eas); Associated with primary ciliary dyskinesia 16.

What condition is associated with DNAL1 p.Ala166= (c.498A>T)?

DNAL1 p.Ala166= (c.498A>T) is associated with primary ciliary dyskinesia 16 (ClinVar).

How common is DNAL1 p.Ala166= (c.498A>T) in the general population?

DNAL1 p.Ala166= (c.498A>T) is ultra-rare (popmax 0.0433%, eas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

DNAL1 p.Ala166=

c.498A>T · rs770681880 · VCV3015499

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0433%, eas)

Conditions

primary ciliary dyskinesia 16

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -1.3	GERP -4.4
Overall
CADD	1.932	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0433% East Asian · 19/43,916 alleles

Filtering AF 0.0282% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0235%

Overall 0.00132% 21/1,585,104 alleles · ultra-rare exomes 20/1,432,864 · genomes 1/152,240 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0433%	2,311
Admixed American	0.00181%	55,304
Remaining individualsnot grpmax-eligible	0.00162%	61,556

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: DNAL1
Protein: p.Ala166=
Coding: c.498A>T
MANE Select: NM_031427
dbSNP: rs770681880
Type: single nucleotide variant
Location: chr14:73689481 (GRCh38)
Gene constraint: LOEUF 1.47 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.81 · 1 PDB
Residue 166: the lrrct domain

Full DNAL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia 16 — 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

DNAL1 p.Asn150Ser Pathogenic ★★ ⚠ same condition
DNAL1 p.Asn67Ser Uncertain significance ★★ ⚠ same condition
DNAL1 p.Glu164Lys Uncertain significance ★★ ⚠ same condition
DNAL1 p.Glu27Asp Uncertain significance ★★ ⚠ same condition
DNAL1 p.Ile34Val Uncertain significance ★★ ⚠ same condition
DNAL1 p.Ser157Ala Uncertain significance ★★ ⚠ same condition
DNAL1 p.Val148Ile Uncertain significance ★★ ⚠ same condition
DNAL1 c.153-12G>C Benign/Likely benign ★★ 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/dnal1-p-ala166 (accessed [today's date]).

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