Is CCDC39 p.Asp99Glu (c.297T>G) pathogenic?

CCDC39 p.Asp99Glu (c.297T>G) is classified Uncertain significance in CCDC39 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-01). AlphaMissense: likely benign (0.104); Ultra-rare (popmax 0.0108%, amr); Associated with primary ciliary dyskinesia.

What condition is associated with CCDC39 p.Asp99Glu (c.297T>G)?

CCDC39 p.Asp99Glu (c.297T>G) is associated with primary ciliary dyskinesia (ClinVar).

How common is CCDC39 p.Asp99Glu (c.297T>G) in the general population?

CCDC39 p.Asp99Glu (c.297T>G) is ultra-rare (popmax 0.0108%, amr) (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 CCDC39 p.Asp99Glu (c.297T>G)?

AlphaMissense predicts likely benign (score 0.104) — an in-silico prediction, not a clinical call.

CCDC39 p.Asp99Glu

c.297T>G · rs763798585 · VCV646484

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.104 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0108%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
AlphaMissense	0.104	likely benign
REVEL	0.131	moderately benign-leaning
SaProt	LLR -5.64	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.062	GERP -3.3
Regional constraint	o/e 0.99	unconstrained · MANE · 64 kb · p 0.72 · regional, not allelic
Overall
CADD	1.11	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0108% Admixed American · 6/55,528 alleles

Filtering AF 0.00467% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00314%

Overall 0.00151% 24/1,584,624 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0108%	9,255
Remaining individualsnot grpmax-eligible	0.00325%	30,759
African / African-American	0.00134%	74,670
European (non-Finnish)	0.00129%	77,567

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.Asp99Glu
Coding: c.297T>G
MANE Select: NM_181426
dbSNP: rs763798585
Type: single nucleotide variant
Location: chr3:180661921 (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.Asp99= Likely benign ★★ same residue
CCDC39 p.Asp99His 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
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-asp99glu (accessed [today's date]).

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