Is DNAH5 p.Phe2484= (c.7452C>T) pathogenic?

DNAH5 p.Phe2484= (c.7452C>T) is classified Likely benign in DNAH5 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-12-10). Ultra-rare (popmax 0.0238%, sas); Associated with primary ciliary dyskinesia.

What condition is associated with DNAH5 p.Phe2484= (c.7452C>T)?

DNAH5 p.Phe2484= (c.7452C>T) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAH5 p.Phe2484= (c.7452C>T) in the general population?

DNAH5 p.Phe2484= (c.7452C>T) is ultra-rare (popmax 0.0238%, sas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

DNAH5 p.Phe2484=

c.7452C>T · rs561666802 · VCV1141971

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0238%, sas)

Conditions

primary ciliary dyskinesia

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 -1.3	GERP -4
Overall
CADD	7.466	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0238% South Asian · 20/84,096 alleles

Filtering AF 0.0157% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0132%

Overall 0.00168% 26/1,550,524 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0238%	4,205
African / African-American	0.00273%	36,570
European (non-Finnish)	0.000349%	286,725

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: DNAH5
Protein: p.Phe2484=
Coding: c.7452C>T
MANE Select: NM_001369
dbSNP: rs561666802
Type: single nucleotide variant
Location: chr5:13810216 (GRCh38)
Gene constraint: LOEUF 0.764 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)

Full DNAH5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia — 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

DNAH5 p.Phe2484Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
DNAH5 p.Phe2484Ser Uncertain significance ★ same residue
DNAH5 c.10555+1G>C Likely pathogenic ★★ same condition
DNAH5 c.1089+1G>A Pathogenic ★★ same condition
DNAH5 c.11028+2T>C Pathogenic/Likely pathogenic ★★ same condition
DNAH5 c.11029-2A>T Pathogenic/Likely pathogenic ★★ same condition
DNAH5 c.11571-1G>A Pathogenic ★★ same condition
DNAH5 c.12910-1G>C 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/dnah5-p-phe2484 (accessed [today's date]).

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