Is CDC20B p.Lys113= (c.339A>G) pathogenic?

CDC20B p.Lys113= (c.339A>G) is classified Likely benign in CDC20B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-01). Rare (popmax 0.11%, nfe).

How common is CDC20B p.Lys113= (c.339A>G) in the general population?

CDC20B p.Lys113= (c.339A>G) is rare (popmax 0.11%, nfe) (gnomAD).

CDC20B p.Lys113=

c.339A>G · rs150714957 · VCV2655462

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.11%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.64	GERP -2.5
Overall
CADD	2.427	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.11% European (non-Finnish) · 1,295/1,179,916 alleles

Filtering AF 0.105% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.103%

Overall 0.0869% 1,403/1,614,032 alleles · rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.122%	822
European (non-Finnish)grpmax	0.11%	911
Admixed American	0.0217%	4,617
African / African-American	0.0173%	5,772
Middle Eastern	0.0165%	6,058
Finnishnot grpmax-eligible	0.00625%	16,009
South Asian	0.0011%	91,072

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CDC20B
Protein: p.Lys113=
Coding: c.339A>G
MANE Select: NM_001170402
dbSNP: rs150714957
Type: single nucleotide variant
Location: chr5:55146644 (GRCh38)
Gene constraint: LOEUF 1.25 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.60
Residue 113: the 'disordered' region

Full CDC20B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GPX8 p.Arg117= Benign ★★ same type
CDC20B p.Ala145Ser Uncertain significance ★ ⚠ same type
CDC20B p.Ala64Val Uncertain significance ★ ⚠ same type
CDC20B p.Arg200Gly Uncertain significance ★ ⚠ same type
CDC20B p.Arg353Pro Uncertain significance ★ ⚠ same type
CDC20B p.Arg7Leu Uncertain significance ★ ⚠ same type
CDC20B p.Asn262Asp Uncertain significance ★ ⚠ same type
CDC20B p.Asn262Ser 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/cdc20b-p-lys113 (accessed [today's date]).

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