Is DNAL1 p.Ser43= (c.129C>T) pathogenic?

DNAL1 p.Ser43= (c.129C>T) is classified Likely benign in DNAL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-10). Absent from gnomAD v4.1; Associated with primary ciliary dyskinesia 16.

What condition is associated with DNAL1 p.Ser43= (c.129C>T)?

DNAL1 p.Ser43= (c.129C>T) is associated with primary ciliary dyskinesia 16 (ClinVar).

How common is DNAL1 p.Ser43= (c.129C>T) in the general population?

DNAL1 p.Ser43= (c.129C>T) is absent from gnomAD v4.1 (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.Ser43=

c.129C>T · rs2140030998 · VCV1625697

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,529,826)

Conditions

primary ciliary dyskinesia 16

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 -0.4	GERP -2.9, phastCons 0.077
Overall
CADD	5.236	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,529,826). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DNAL1
Protein: p.Ser43=
Coding: c.129C>T
MANE Select: NM_031427
dbSNP: rs2140030998
Type: single nucleotide variant
Location: chr14:73658933 (GRCh38)
Gene constraint: LOEUF 1.47 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.81 · 1 PDB

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-ser43 (accessed [today's date]).

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