Is CCDC39 p.Lys336= (c.1008G>A) pathogenic?

CCDC39 p.Lys336= (c.1008G>A) is classified Benign/Likely benign in CCDC39 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-31). Low-frequency (popmax 4.34%, eas); Associated with primary ciliary dyskinesia 14.

What condition is associated with CCDC39 p.Lys336= (c.1008G>A)?

CCDC39 p.Lys336= (c.1008G>A) is associated with primary ciliary dyskinesia 14, primary ciliary dyskinesia (ClinVar).

How common is CCDC39 p.Lys336= (c.1008G>A) in the general population?

CCDC39 p.Lys336= (c.1008G>A) is low-frequency (popmax 4.34%, 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.Lys336=

c.1008G>A · rs79329972 · VCV262960

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

low-frequency (popmax 4.34%, eas)

Conditions

primary ciliary dyskinesia 14

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 2.1	GERP 1.4, phastCons 1
Overall
CADD	6.459	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.34% East Asian · 1,737/40,000 alleles

Filtering AF 4.17% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.1%

Overall 0.208% 3,173/1,528,792 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	4.34%	23
Finnishnot grpmax-eligible	0.944%	106
Remaining individualsnot grpmax-eligible	0.213%	470
Ashkenazi Jewishnot grpmax-eligible	0.134%	746
Middle Eastern	0.106%	942
South Asian	0.0929%	1,077
European (non-Finnish)	0.0539%	1,855
Admixed American	0.0248%	4,027
African / African-American	0.00971%	10,302

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.Lys336=
Coding: c.1008G>A
MANE Select: NM_181426
dbSNP: rs79329972
Type: single nucleotide variant
Location: chr3:180652189 (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 14 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: primary ciliary dyskinesia

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.Lys336Ter Pathogenic ★ same residue
CCDC39 p.Lys336fs Pathogenic ★ 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
CCDC39 c.357+1G>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-lys336 (accessed [today's date]).

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