Is DNAH9 p.Pro143= (c.429C>T) pathogenic?

DNAH9 p.Pro143= (c.429C>T) is classified Benign in DNAH9 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-04). Common (popmax 60.4%, sas) — too common for a highly-penetrant pathogenic allele; Associated with ciliary dyskinesia, primary, 40.

What condition is associated with DNAH9 p.Pro143= (c.429C>T)?

DNAH9 p.Pro143= (c.429C>T) 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.Pro143=

Q: How common is DNAH9 p.Pro143= (c.429C>T) in the general population?

DNAH9 p.Pro143= (c.429C>T) is common (popmax 60.4%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.429C>T · rs11078022 · VCV402773

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 60.4%, sas) — 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 -4.3	GERP -5
Overall
CADD	0.641	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 60.4% South Asian · 54,165/89,700 alleles

Filtering AF 60% ClinGen BA1/BS1 input FAF95, joint · FAF99 59.8%

Overall 41.8% 666,109/1,594,930 alleles · common

Ancestry group	Frequency	1 in
South Asiangrpmax	60.4%	2
Admixed American	59.8%	2
East Asian	58%	2
Middle Eastern	51.2%	2
Ashkenazi Jewishnot grpmax-eligible	47.9%	2
Remaining individualsnot grpmax-eligible	43.1%	2
European (non-Finnish)	40.2%	2
Finnishnot grpmax-eligible	37.8%	3
Amishnot grpmax-eligible	34.4%	3
African / African-American	19.8%	5

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.Pro143=
Coding: c.429C>T
MANE Select: NM_001372
dbSNP: rs11078022
Type: single nucleotide variant
Location: chr17:11608140 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 (gnomAD)
Residue 143: 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-pro143 (accessed [today's date]).

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