Is CDC20 p.Cys364Ter (c.1092T>A) pathogenic?

CDC20 p.Cys364Ter (c.1092T>A) is classified Likely pathogenic in CDC20 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-17). Very rare (popmax 0.00329%, sas); Associated with oocyte maturation defect 14.

What condition is associated with CDC20 p.Cys364Ter (c.1092T>A)?

CDC20 p.Cys364Ter (c.1092T>A) is associated with oocyte maturation defect 14 (ClinVar).

How common is CDC20 p.Cys364Ter (c.1092T>A) in the general population?

CDC20 p.Cys364Ter (c.1092T>A) is very rare (popmax 0.00329%, sas) (gnomAD).

CDC20 p.Cys364Ter

c.1092T>A · VCV4850379

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 0.00329%, sas)

Conditions

oocyte maturation defect 14

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 9 of 11
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.1	GERP 2.2, phastCons 1
Overall
CADD	39.0	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 0.00329% South Asian · 3/91,064 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.000205% 3/1,461,852 alleles · very rare

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: CDC20
Protein: p.Cys364Ter
Coding: c.1092T>A
MANE Select: NM_001255
Type: single nucleotide variant
Location: chr1:43361134 (GRCh38)
Gene constraint: LOEUF 0.744 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.39 · 17 PDB
Residue 364: a UniProt-annotated variant site (in ozema14; severely decreased function in metaphase/anaphase transition of meiosis i; does not fully rescue metaphase i arrest in cdc20-knocked down mouse oocytes; decreased function in positive regulation of anaphase-promoting complex-dependent catabolic process; fails to localize to the kinetochore); a UniProt-annotated variant site (in ozema14)

Full CDC20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

oocyte maturation defect 14 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDC20 c.556+1G>T Conflicting classifications of pathogenicity ★ same condition
CDC20 c.330+1G>A Pathogenic same condition
CDC20 p.Ala211Thr Pathogenic ⚠ same condition
CDC20 p.Arg182Ter Pathogenic same condition
CDC20 p.Arg262Ter Pathogenic same condition
CDC20 p.Arg322Gln Pathogenic ⚠ same condition
CDC20 p.Arg322Ter Pathogenic same condition
CDC20 p.Trp385Cys 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/cdc20-p-cys364ter (accessed [today's date]).

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