Is DNAH9 p.Phe103fs (c.308del) pathogenic?

DNAH9 p.Phe103fs (c.308del) is classified Pathogenic/Likely pathogenic in DNAH9 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2025-03-18). Ultra-rare (popmax 0.0688%, nfe); Associated with DNAH9-related disorder.

What condition is associated with DNAH9 p.Phe103fs (c.308del)?

DNAH9 p.Phe103fs (c.308del) is associated with DNAH9-related disorder, primary ciliary dyskinesia, ciliary dyskinesia, primary, 40 (ClinVar).

How common is DNAH9 p.Phe103fs (c.308del) in the general population?

DNAH9 p.Phe103fs (c.308del) is ultra-rare (popmax 0.0688%, nfe) (gnomAD).

DNAH9 p.Phe103fs

c.308del · rs769795916 · VCV1455970

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0688%, nfe)

Conditions

DNAH9-related disorder

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 1 of 69
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.6	GERP -0.049, phastCons 0.88
Overall
CADD	24.5	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

Grpmax group 0.0688% European (non-Finnish) · 770/1,118,860 alleles

Filtering AF 0.0648% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0632%

Overall 0.06% 888/1,479,728 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0688%	1,453
Remaining individualsnot grpmax-eligible	0.0457%	2,190
African / African-American	0.038%	2,633
South Asian	0.0351%	2,845
Ashkenazi Jewishnot grpmax-eligible	0.0347%	2,886
East Asian	0.0309%	3,238
Admixed American	0.0279%	3,589
Finnishnot grpmax-eligible	0.0134%	7,477

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: DNAH9
Protein: p.Phe103fs
Coding: c.308del
MANE Select: NM_001372
dbSNP: rs769795916
Type: Deletion
Location: chr17:11598800 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 (gnomAD)
Residue 103: the 'stem' region

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

Disease context

DNAH9-related disorder

Also linked: primary ciliary dyskinesia ciliary dyskinesia, primary, 40

Similar variants

DNAH9 c.3354-1del Likely pathogenic ★★ same condition
DNAH9 p.Asn780fs Pathogenic/Likely pathogenic ★★ same condition
DNAH9 p.Glu2765fs Pathogenic/Likely pathogenic ★★ same condition
DNAH9 p.Leu578fs Pathogenic/Likely pathogenic ★★ same condition
DNAH9 p.Phe254fs Pathogenic/Likely pathogenic ★★ same condition
DNAH9 p.Pro2957fs Likely pathogenic ★★ same condition
DNAH9 p.Tyr4107fs Pathogenic/Likely pathogenic ★★ same condition
DNAH9 p.Phe103Cys Likely benign ★★ ⚠ same residue

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-phe103fs (accessed [today's date]).

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