Is DNAH5 p.Ala1024= (c.3072C>T) pathogenic?

DNAH5 p.Ala1024= (c.3072C>T) is classified Likely benign in DNAH5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-23). Very rare (popmax 0.00167%, amr); Associated with primary ciliary dyskinesia.

What condition is associated with DNAH5 p.Ala1024= (c.3072C>T)?

DNAH5 p.Ala1024= (c.3072C>T) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAH5 p.Ala1024= (c.3072C>T) in the general population?

DNAH5 p.Ala1024= (c.3072C>T) is very rare (popmax 0.00167%, amr) (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.Ala1024=

c.3072C>T · rs759791781 · VCV1136637

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

primary ciliary dyskinesia

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.013	GERP -3.3
Overall
CADD	1.269	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,994 alleles

Overall 6.2e-05% 1/1,613,986 alleles · very rare exomes 0/1,461,866 · genomes 1/152,120 · joint denominator

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.Ala1024=
Coding: c.3072C>T
MANE Select: NM_001369
dbSNP: rs759791781
Type: single nucleotide variant
Location: chr5:13883006 (GRCh38)

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)

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-ala1024 (accessed [today's date]).

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