Is CCDC82 p.Arg237Ter (c.709C>T) pathogenic?

CCDC82 p.Arg237Ter (c.709C>T) is classified Likely pathogenic in CCDC82 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2025-03-02). Absent from gnomAD v4.1; Associated with CCDC82-related disorder.

What condition is associated with CCDC82 p.Arg237Ter (c.709C>T)?

CCDC82 p.Arg237Ter (c.709C>T) is associated with CCDC82-related disorder (ClinVar).

How common is CCDC82 p.Arg237Ter (c.709C>T) in the general population?

CCDC82 p.Arg237Ter (c.709C>T) is absent from gnomAD v4.1 (gnomAD).

CCDC82 p.Arg237Ter

c.709C>T · VCV3777029

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

CCDC82-related disorder

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 2.4	GERP 1, phastCons 0.062
Overall
CADD	35.0	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CCDC82
Protein: p.Arg237Ter
Coding: c.709C>T
MANE Select: NM_024725
Type: single nucleotide variant
Location: chr11:96384039 (GRCh38)
Gene constraint: LOEUF 1.06 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.94
Residue 237: the 'disordered' region

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

Disease context

CCDC82-related disorder

Similar variants

CCDC82 p.Arg237Gln Uncertain significance ★ ⚠ same residue
CCDC82 p.Lys403Ter Uncertain significance ★ same condition
CCDC82 p.Thr108Ala Benign ★★ same type
CCDC82 p.Arg23Ter Likely pathogenic ★ 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

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-arg237ter (accessed [today's date]).

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