Is DNAH5 p.Arg982Cys (c.2944C>T) pathogenic?

DNAH5 p.Arg982Cys (c.2944C>T) is classified Conflicting classifications of pathogenicity in DNAH5 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-05-27). AlphaMissense: likely benign (0.2715); Ultra-rare (popmax 0.0165%, mid); Associated with primary ciliary dyskinesia.

What condition is associated with DNAH5 p.Arg982Cys (c.2944C>T)?

DNAH5 p.Arg982Cys (c.2944C>T) is associated with primary ciliary dyskinesia (ClinVar).

How common is DNAH5 p.Arg982Cys (c.2944C>T) in the general population?

DNAH5 p.Arg982Cys (c.2944C>T) is ultra-rare (popmax 0.0165%, mid) (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.Arg982Cys (c.2944C>T)?

AlphaMissense predicts likely benign (score 0.2715) — an in-silico prediction, not a clinical call.

DNAH5 p.Arg982Cys

c.2944C>T · rs143673459 · VCV454762

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2715 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
AlphaMissense	0.2715	likely benign
REVEL	0.448	indeterminate
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 228 kb · p 0.16 · regional, not allelic
Overall
CADD	25.1	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 0.0165% Middle Eastern · 1/6,062 alleles

Filtering AF 0.00622% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00467%

Overall 0.00167% 27/1,614,192 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,062
African / African-American	0.012%	8,340
Admixed American	0.005%	20,009
East Asian	0.00223%	44,880
Finnishnot grpmax-eligible	0.00156%	64,032
European (non-Finnish)	0.00102%	98,335

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.Arg982Cys
Coding: c.2944C>T
dbSNP: rs143673459
Type: single nucleotide variant
Location: chr5:13885028 (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-arg982cys (accessed [today's date]).

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