Is DNAH9 p.Asp3105Val (c.9314A>T) pathogenic?

DNAH9 p.Asp3105Val (c.9314A>T) is classified Uncertain significance in DNAH9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-10). AlphaMissense: likely benign (0.2344); Very rare (popmax 8.47e-05%, nfe); Associated with ciliary dyskinesia, primary, 40.

What condition is associated with DNAH9 p.Asp3105Val (c.9314A>T)?

DNAH9 p.Asp3105Val (c.9314A>T) is associated with ciliary dyskinesia, primary, 40 (ClinVar).

How common is DNAH9 p.Asp3105Val (c.9314A>T) in the general population?

DNAH9 p.Asp3105Val (c.9314A>T) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

What do computational predictors say about DNAH9 p.Asp3105Val (c.9314A>T)?

AlphaMissense predicts likely benign (score 0.2344) — an in-silico prediction, not a clinical call.

DNAH9 p.Asp3105Val

c.9314A>T · VCV4278027

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2344 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, REVEL

Conditions

ciliary dyskinesia, primary, 40

Computational evidence

Protein change
AlphaMissense	0.2344	likely benign
REVEL	0.852	moderately pathogenic-leaning
⇒ REVEL calls this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.2, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 333 kb · p 0.00016 · regional, not allelic
Overall
CADD	25.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,179,998 alleles

Overall 6.84e-05% 1/1,461,784 alleles · very rare

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.Asp3105Val
Coding: c.9314A>T
MANE Select: NM_001372
Type: single nucleotide variant
Location: chr17:11834705 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 (gnomAD)
Residue 3105: a UniProt-annotated variant site (in cild40); a UniProt-annotated variant site (in cild40; loss of localization to cilium axonema); the 'stalk' 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 p.Asp3105Gly Uncertain significance ★★ ⚠ same residue
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

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-asp3105val (accessed [today's date]).

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