Is DNAH17 p.Pro403= (c.1209C>T) pathogenic?

DNAH17 p.Pro403= (c.1209C>T) is classified Likely benign in DNAH17 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-28). Very rare (popmax 0.00267%, afr); Associated with DNAH17-related disorder.

What condition is associated with DNAH17 p.Pro403= (c.1209C>T)?

DNAH17 p.Pro403= (c.1209C>T) is associated with DNAH17-related disorder (ClinVar).

How common is DNAH17 p.Pro403= (c.1209C>T) in the general population?

DNAH17 p.Pro403= (c.1209C>T) is very rare (popmax 0.00267%, afr) (gnomAD).

DNAH17 p.Pro403=

c.1209C>T · rs769572675 · VCV3047904

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

DNAH17-related disorder

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 -20	GERP -3.1
Overall
CADD	0.281	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,802 alleles

Filtering AF 0.00181% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00157%

Overall 0.0023% 37/1,606,532 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,401
European (non-Finnish)	0.00255%	39,218
East Asian	0.00224%	44,724
South Asian	0.00224%	44,735
Admixed American	0.0017%	58,748
Remaining individualsnot grpmax-eligible	0.00161%	62,260

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: DNAH17
Protein: p.Pro403=
Coding: c.1209C>T
MANE Select: NM_173628
dbSNP: rs769572675
Type: single nucleotide variant
Location: chr17:78569241 (GRCh38)
Gene constraint: LOEUF 0.859 · pLI <0.01 (gnomAD)
Residue 403: the 'stem' region

Full DNAH17 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNAH17-related disorder

Similar variants

DNAH17 c.6818+1G>A Likely pathogenic same condition
DNAH17 p.Ala2154Thr Uncertain significance ⚠ same condition
DNAH17 c.10735-5T>G Likely benign same condition
DNAH17 c.11212-7C>T Likely benign same condition
DNAH17 c.11334+4C>T Likely benign same condition
DNAH17 c.11805+5G>A Likely benign same condition
DNAH17 c.12915+7G>T Benign same condition
DNAH17 c.1836-10C>G Likely benign 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/dnah17-p-pro403 (accessed [today's date]).

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