CC2D2A

Chr 4AR

coiled-coil and C2 domain containing 2A

Also known as: COACH2, JBTS9, MKS6, RP93

This gene encodes a coiled-coil and calcium binding domain protein that appears to play a critical role in cilia formation. Mutations in this gene cause Meckel syndrome type 6, as well as Joubert syndrome type 9. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

OMIMResearchGenerating clinical summary…
LOFmechanismARLOEUF 0.784 OMIM phenotypes
Clinical SummaryCC2D2A
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Gene-Disease Validity (ClinGen)
ciliopathy · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
0.78LOEUF
pLI 0.000
Z-score 3.32
OE 0.63 (0.510.78)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.65Z-score
OE missense 0.94 (0.880.99)
758 obs / 809.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.63 (0.510.78)
00.351.4
Missense OE?0.94 (0.880.99)
00.61.4
Synonymous OE?0.96
01.21.6
LoF obs/exp: 58 / 92.4Missense obs/exp: 758 / 809.8Syn Z: 0.55
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveCC2D2A-related Joubert syndromeLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6260th %ile
GOF
0.6247th %ile
LOF
0.3355th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

CC2D2A · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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