Is CCDC82 p.Arg23Ter (c.67C>T) pathogenic?

CCDC82 p.Arg23Ter (c.67C>T) is classified Likely pathogenic in CCDC82 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-04). Very rare (popmax 0.00223%, eas); Associated with intellectual disability.

What condition is associated with CCDC82 p.Arg23Ter (c.67C>T)?

CCDC82 p.Arg23Ter (c.67C>T) is associated with intellectual disability (ClinVar).

How common is CCDC82 p.Arg23Ter (c.67C>T) in the general population?

CCDC82 p.Arg23Ter (c.67C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

CCDC82 p.Arg23Ter

c.67C>T · rs1866090527 · VCV1708245

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Conditions

intellectual disability

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 10
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.8	GERP 2, phastCons 1
Overall
CADD	37.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,844 alleles

Overall 0.000137% 2/1,460,920 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,844
European (non-Finnish)	8.48e-05%	1,179,530

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: CCDC82
Protein: p.Arg23Ter
Coding: c.67C>T
MANE Select: NM_024725
dbSNP: rs1866090527
Type: single nucleotide variant
Location: chr11:96384681 (GRCh38)
Gene constraint: LOEUF 1.06 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.94
Residue 23: the 'disordered' region

Full CCDC82 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CCDC82 p.Arg23Gln Uncertain significance ★ ⚠ same residue
CCDC82 p.Thr108Ala Benign ★★ same type
CCDC82 p.Ala233Thr Uncertain significance ★ ⚠ same type
CCDC82 p.Ala351Thr Uncertain significance ★ ⚠ same type
CCDC82 p.Arg11Gly Uncertain significance ★ ⚠ same type
CCDC82 p.Arg179Gln Uncertain significance ★ ⚠ same type
CCDC82 p.Arg179Ter Conflicting classifications of pathogenicity ★ same type
CCDC82 p.Arg211Cys Uncertain significance ★ ⚠ same type

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/ccdc82-p-arg23ter (accessed [today's date]).

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