Is DNAH9 p.Phe102= (c.306T>C) pathogenic?

DNAH9 p.Phe102= (c.306T>C) is classified Benign/Likely benign in DNAH9 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-28). Common (popmax 5.46%, afr) — too common for a highly-penetrant pathogenic allele; Associated with ciliary dyskinesia, primary, 40.

What condition is associated with DNAH9 p.Phe102= (c.306T>C)?

DNAH9 p.Phe102= (c.306T>C) is associated with ciliary dyskinesia, primary, 40 (ClinVar).

How is Primary ciliary dyskinesia inherited?

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

DNAH9 p.Phe102=

Q: How common is DNAH9 p.Phe102= (c.306T>C) in the general population?

DNAH9 p.Phe102= (c.306T>C) is common (popmax 5.46%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.306T>C · rs28507962 · VCV1273191

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 5.46%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

ciliary dyskinesia, primary, 40

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.13	GERP -3.7, phastCons 0.76
Overall
CADD	1.722	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.46% African / African-American · 3,732/68,370 alleles

Filtering AF 5.31% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.25%

Overall 0.276% 4,094/1,480,796 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.46%	18
Admixed American	0.327%	306
Remaining individualsnot grpmax-eligible	0.311%	322
Middle Eastern	0.128%	782
European (non-Finnish)	0.00313%	31,990
East Asian	0.00281%	35,604
South Asian	0.0025%	39,941

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.Phe102=
Coding: c.306T>C
MANE Select: NM_001372
dbSNP: rs28507962
Type: single nucleotide variant
Location: chr17:11598804 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 (gnomAD)
Residue 102: 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 p.Phe102Val 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-phe102 (accessed [today's date]).

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