Is DNAH5 p.Glu3293Ala (c.9878A>C) pathogenic?

DNAH5 p.Glu3293Ala (c.9878A>C) is classified Conflicting classifications of pathogenicity in DNAH5 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-05-29). AlphaMissense: likely benign (0.1114); Ultra-rare (popmax 0.0143%, sas); Associated with primary ciliary dyskinesia.

What condition is associated with DNAH5 p.Glu3293Ala (c.9878A>C)?

DNAH5 p.Glu3293Ala (c.9878A>C) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAH5 p.Glu3293Ala (c.9878A>C) in the general population?

DNAH5 p.Glu3293Ala (c.9878A>C) is ultra-rare (popmax 0.0143%, sas) (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 DNAH5 p.Glu3293Ala (c.9878A>C)?

AlphaMissense predicts likely benign (score 0.1114) — an in-silico prediction, not a clinical call.

DNAH5 p.Glu3293Ala

c.9878A>C · rs542064804 · VCV2197550

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1114 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0143%, sas)

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
AlphaMissense	0.1114	likely benign
REVEL	0.339	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP 2.8, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 228 kb · p 0.16 · regional, not allelic
Overall
CADD	21.9	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 0.0143% South Asian · 13/91,088 alleles

Filtering AF 0.00844% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00661%

Overall 0.0013% 21/1,614,192 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0143%	7,007
Remaining individualsnot grpmax-eligible	0.0096%	10,417
Finnishnot grpmax-eligible	0.00312%	32,022

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.Glu3293Ala
Coding: c.9878A>C
MANE Select: NM_001369
dbSNP: rs542064804
Type: single nucleotide variant
Location: chr5:13768979 (GRCh38)
Gene constraint: LOEUF 0.764 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 3293: the 'stalk' region

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.Glu3293Ter Pathogenic ★ same residue
DNAH5 p.Glu3293= Likely benign ★ 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-glu3293ala (accessed [today's date]).

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