Is DNAH9 p.Trp428Ter (c.1284G>A) pathogenic?

DNAH9 p.Trp428Ter (c.1284G>A) is classified Likely pathogenic in DNAH9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-03). Absent from gnomAD v4.1; Associated with ciliary dyskinesia, primary, 40.

What condition is associated with DNAH9 p.Trp428Ter (c.1284G>A)?

DNAH9 p.Trp428Ter (c.1284G>A) is associated with ciliary dyskinesia, primary, 40 (ClinVar).

How common is DNAH9 p.Trp428Ter (c.1284G>A) in the general population?

DNAH9 p.Trp428Ter (c.1284G>A) 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.

DNAH9 p.Trp428Ter

c.1284G>A · VCV4081342

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

ciliary dyskinesia, primary, 40

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 6 of 69
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Overall
CADD	39.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DNAH9
Protein: p.Trp428Ter
Coding: c.1284G>A
MANE Select: NM_001372
Type: single nucleotide variant
Location: chr17:11619715 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 (gnomAD)
Residue 428: the 'stem' region

Full DNAH9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ciliary dyskinesia, primary, 40 — 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

DNAH9 c.11406+1G>T Likely pathogenic ★★ same condition
DNAH9 c.1901+1G>A Likely pathogenic ★★ same condition
DNAH9 c.615-2A>G Likely pathogenic ★★ same condition
DNAH9 c.6847+1G>A Likely pathogenic ★★ same condition
DNAH9 p.Arg1344Ter Pathogenic/Likely pathogenic ★★ same condition
DNAH9 p.Arg1517Ter Pathogenic/Likely pathogenic ★★ same condition
DNAH9 p.Arg1640Ter Likely pathogenic ★★ same condition
DNAH9 p.Arg24Ter 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/dnah9-p-trp428ter (accessed [today's date]).

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