Is CCDC39 p.Arg103= (c.307C>A) pathogenic?

CCDC39 p.Arg103= (c.307C>A) is classified Likely benign in CCDC39 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-11-20). Very rare (popmax 0.0068%, eas); Associated with primary ciliary dyskinesia.

What condition is associated with CCDC39 p.Arg103= (c.307C>A)?

CCDC39 p.Arg103= (c.307C>A) is associated with primary ciliary dyskinesia (ClinVar).

How common is CCDC39 p.Arg103= (c.307C>A) in the general population?

CCDC39 p.Arg103= (c.307C>A) is very rare (popmax 0.0068%, eas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

CCDC39 p.Arg103=

c.307C>A · rs61733582 · VCV1727346

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0068%, eas)

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 1.7	GERP -0.91, phastCons 0.029
Overall
CADD	1.502	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0068% East Asian · 3/44,136 alleles

Filtering AF 0.0018% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0009%

Overall 0.000378% 6/1,587,094 alleles · very rare exomes 4/1,435,162 · genomes 2/151,932 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0068%	14,712
Remaining individualsnot grpmax-eligible	0.00325%	30,779
European (non-Finnish)	8.58e-05%	1,165,022

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: CCDC39
Protein: p.Arg103=
Coding: c.307C>A
MANE Select: NM_181426
dbSNP: rs61733582
Type: single nucleotide variant
Location: chr3:180661911 (GRCh38)
Gene constraint: LOEUF 1.226 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 79.23 · 1 PDB

Full CCDC39 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

CCDC39 p.Arg103Trp Uncertain significance ★★ ⚠ same residue
CCDC39 p.Arg103Gln Uncertain significance ★ ⚠ same residue
CCDC39 p.Arg103Pro Uncertain significance ★ ⚠ same residue
CCDC39 c.1034+2T>A Pathogenic/Likely pathogenic ★★ same condition
CCDC39 c.1167+1261A>G Pathogenic/Likely pathogenic ★★ same condition
CCDC39 c.1362+1G>A Likely pathogenic ★★ same condition
CCDC39 c.1999-2A>T Pathogenic/Likely pathogenic ★★ same condition
CCDC39 c.210+2T>C 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/ccdc39-p-arg103 (accessed [today's date]).

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