Is DNAH5 p.Leu1007fs (c.3020del) pathogenic?

DNAH5 p.Leu1007fs (c.3020del) is classified Pathogenic/Likely pathogenic in DNAH5 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-24). Absent from gnomAD; Associated with primary ciliary dyskinesia.

What condition is associated with DNAH5 p.Leu1007fs (c.3020del)?

DNAH5 p.Leu1007fs (c.3020del) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAH5 p.Leu1007fs (c.3020del) in the general population?

DNAH5 p.Leu1007fs (c.3020del) 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.Leu1007fs

c.3020del · rs1771899943 · VCV1073021

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

primary ciliary dyskinesia

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 20 of 79
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.7	GERP -2

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.Leu1007fs
Coding: c.3020del
MANE Select: NM_001369
dbSNP: rs1771899943
Type: Deletion
Location: chr5:13883058 (GRCh38)
Gene constraint: LOEUF 0.764 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1007: the 'stem' region

Full DNAH5 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

DNAH5 p.Leu1007Phe Benign/Likely benign ★★ same residue
DNAH5 c.2577+2del Likely pathogenic ★★ same condition
DNAH5 c.54_57+5del Likely pathogenic ★★ same condition
DNAH5 c.9605+1del Pathogenic/Likely pathogenic ★★ same condition
DNAH5 p.Ala1977fs Pathogenic ★★ same condition
DNAH5 p.Ala278fs Pathogenic/Likely pathogenic ★★ same condition
DNAH5 p.Ala3121_Leu3122insTer Pathogenic/Likely pathogenic ★★ same condition
DNAH5 p.Ala318fs 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-leu1007fs (accessed [today's date]).

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