Is CDC20B p.Ser208Arg (c.624T>G) pathogenic?

CDC20B p.Ser208Arg (c.624T>G) is classified Likely benign in CDC20B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-07). AlphaMissense: likely benign (0.0588); Very rare (popmax 0.00234%, sas).

How common is CDC20B p.Ser208Arg (c.624T>G) in the general population?

CDC20B p.Ser208Arg (c.624T>G) is very rare (popmax 0.00234%, sas) (gnomAD).

What do computational predictors say about CDC20B p.Ser208Arg (c.624T>G)?

AlphaMissense predicts likely benign (score 0.0588) — an in-silico prediction, not a clinical call.

CDC20B p.Ser208Arg

c.624T>G · rs745338696 · VCV2471534

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0588 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00234%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0588	likely benign
REVEL	0.019	moderately benign-leaning
SaProt	LLR -7.09	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.6	GERP -2.6
Regional constraint	o/e 0.89	unconstrained · MANE · 19 kb · p 0.027 · regional, not allelic
Overall
CADD	0.375	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00234% South Asian · 2/85,558 alleles

Filtering AF 0.000437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000319%

Overall 0.00076% 12/1,579,594 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00234%	42,779
European (non-Finnish)	0.000864%	115,695

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.Ser208Arg
Coding: c.624T>G
MANE Select: NM_001170402
dbSNP: rs745338696
Type: single nucleotide variant
Location: chr5:55133485 (GRCh38)
Gene constraint: LOEUF 1.25 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.60

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-ser208arg (accessed [today's date]).

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