Is CDC42BPB p.Ser650= (c.1950C>T) pathogenic?

CDC42BPB p.Ser650= (c.1950C>T) is classified Likely benign in CDC42BPB (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-02-15). Ultra-rare (popmax 0.0166%, mid); Associated with CDC42BPB-related disorder.

What condition is associated with CDC42BPB p.Ser650= (c.1950C>T)?

CDC42BPB p.Ser650= (c.1950C>T) is associated with CDC42BPB-related disorder (ClinVar).

How common is CDC42BPB p.Ser650= (c.1950C>T) in the general population?

CDC42BPB p.Ser650= (c.1950C>T) is ultra-rare (popmax 0.0166%, mid) (gnomAD).

CDC42BPB p.Ser650=

c.1950C>T · rs1413235617 · VCV3028980

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0166%, mid)

Conditions

CDC42BPB-related disorder

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 -1.5	GERP -4.2
Overall
CADD	7.225	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0166% Middle Eastern · 1/6,042 alleles

Filtering AF 0.000292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000806% 13/1,613,796 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0166%	6,042
Remaining individualsnot grpmax-eligible	0.0032%	31,234
Admixed American	0.00167%	59,984
South Asian	0.0011%	91,016
European (non-Finnish)	0.000678%	147,499

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: CDC42BPB
Protein: p.Ser650=
Coding: c.1950C>T
MANE Select: NM_006035
dbSNP: rs1413235617
Type: single nucleotide variant
Location: chr14:102970196 (GRCh38)
Gene constraint: LOEUF 0.235 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 76.28 · 6 PDB

Full CDC42BPB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CDC42BPB-related disorder

Similar variants

CDC42BPB p.Ser650Asn Uncertain significance ★ ⚠ same residue
CDC42BPB p.Ser650Gly Uncertain significance ★ ⚠ same residue
CDC42BPB p.Arg867Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDC42BPB p.Arg876Pro Likely pathogenic ★★ ⚠ same condition
CDC42BPB p.Asp175Tyr Likely pathogenic ★★ same condition
CDC42BPB p.Arg1299Gln Likely pathogenic ★ ⚠ same condition
CDC42BPB p.Arg1350Pro Likely pathogenic ★ same condition
CDC42BPB p.Arg876Trp Likely 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/cdc42bpb-p-ser650 (accessed [today's date]).

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