Is DNAH5 p.Ala1939fs (c.5815_5821del) pathogenic?

DNAH5 p.Ala1939fs (c.58155821del) is classified Likely pathogenic in DNAH5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-22). Absent from gnomAD; Associated with primary ciliary dyskinesia 3.

What condition is associated with DNAH5 p.Ala1939fs (c.5815_5821del)?

DNAH5 p.Ala1939fs (c.5815_5821del) is associated with primary ciliary dyskinesia 3 (ClinVar).

How common is DNAH5 p.Ala1939fs (c.5815_5821del) in the general population?

DNAH5 p.Ala1939fs (c.5815_5821del) is absent from gnomAD (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

DNAH5 p.Ala1939fs

c.5815_5821del · rs2546902882 · VCV1724616

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

primary ciliary dyskinesia 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 35 of 79
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.48	GERP -5

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: DNAH5
Protein: p.Ala1939fs
Coding: c.5815_5821del
MANE Select: NM_001369
dbSNP: rs2546902882
Type: Deletion
Location: chr5:13839417 (GRCh38)
Gene constraint: LOEUF 0.764 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1939: the 'stem' region

Full DNAH5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia 3 — 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

DNAH5 p.Ala1939= Conflicting classifications of pathogenicity ★ same residue
DNAH5 c.54_57+5del Likely pathogenic ★★ same condition
DNAH5 c.7609+1_7609+3del Pathogenic/Likely pathogenic ★★ same condition
DNAH5 p.Ala278fs Pathogenic/Likely pathogenic ★★ same condition
DNAH5 p.Ala3121_Leu3122insTer Pathogenic/Likely pathogenic ★★ same condition
DNAH5 p.Ala4354fs Pathogenic/Likely pathogenic ★★ same condition
DNAH5 p.Arg3000fs Pathogenic/Likely pathogenic ★★ same condition
DNAH5 p.Asn1438fs Pathogenic/Likely pathogenic ★★ 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/dnah5-p-ala1939fs (accessed [today's date]).

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