CCDC82

Chr 11

coiled-coil domain containing 82

Also known as: HSPC048

NCBI Gene: 79780 ENSG00000149231 UniProt: Q8N4S0

The CCDC82 protein is predicted to be active in the nucleus, though its specific function remains unclear. Mutations in this gene have been associated with neurodevelopmental disorders, though the clinical phenotype and inheritance pattern are not well-established in the current literature. This gene shows tolerance to loss-of-function variants based on population genetic data.

ResearchSummary from RefSeq

Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

DNmechanismLOEUF 0.86

Clinical Summary— CCDC82

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Population Constraint (gnomAD)

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

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ClinVar Variants

3 unique Pathogenic / Likely Pathogenic· 82 VUS of 108 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.86LOEUF

pLI 0.000

Z-score 2.14

OE 0.56 (0.37–0.86)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.08Z-score

OE missense 0.99 (0.89–1.09)

275 obs / 278.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.56 (0.37–0.86)

0≤0.351.4

Missense OE?0.99 (0.89–1.09)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 15 / 27.0Missense obs/exp: 275 / 278.9Syn Z: 0.35

This gene — mechanism propensity

0.7132th %ile

GOF

0.3689th %ile

LOF

0.2775th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

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

ClinVar Variant Classifications

108 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

Likely Pathogenic2

VUS82

Likely Benign8

Benign1

Conflicting1

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	1	0	0	0	1
Likely Pathogenic	2	0	0	0	2
VUS	6	76	0	0	82
Likely Benign	0	7	0	1	8
Benign	0	1	0	0	1
Conflicting	—				1
Total	9	84	0	1	95

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

15 pathogenic / likely-pathogenic (of 19) ClinVar copy-number / structural variants overlap CCDC82 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →