Is CDC42BPB p.Asp1069Glu (c.3207C>A) pathogenic?

CDC42BPB p.Asp1069Glu (c.3207C>A) is classified Likely benign in CDC42BPB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-08). AlphaMissense: likely benign (0.0847); Ultra-rare (popmax 0.0402%, afr); Associated with Inborn genetic diseases.

What condition is associated with CDC42BPB p.Asp1069Glu (c.3207C>A)?

CDC42BPB p.Asp1069Glu (c.3207C>A) is associated with Inborn genetic diseases (ClinVar).

How common is CDC42BPB p.Asp1069Glu (c.3207C>A) in the general population?

CDC42BPB p.Asp1069Glu (c.3207C>A) is ultra-rare (popmax 0.0402%, afr) (gnomAD).

What do computational predictors say about CDC42BPB p.Asp1069Glu (c.3207C>A)?

AlphaMissense predicts likely benign (score 0.0847) — an in-silico prediction, not a clinical call.

CDC42BPB p.Asp1069Glu

c.3207C>A · VCV4223305

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0847 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0402%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0847	likely benign
REVEL	0.234	benign-leaning
SaProt	LLR -6.55	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 3.8	GERP 0.73, phastCons 1
Regional constraint	o/e 0.72	unconstrained · MANE · 15 kb · p 2e-15 · regional, not allelic
Overall
CADD	19.44	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 0.0402% African / African-American · 30/74,606 alleles

Filtering AF 0.0289% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.025%

Overall 0.00231% 37/1,604,752 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0402%	2,487
Admixed American	0.00171%	58,554
Remaining individualsnot grpmax-eligible	0.00161%	62,056
European (non-Finnish)	0.000425%	235,143

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.Asp1069Glu
Coding: c.3207C>A
MANE Select: NM_006035
Type: single nucleotide variant
Location: chr14:102950568 (GRCh38)
Gene constraint: LOEUF 0.235 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 76.28 · 6 PDB
Residue 1069: a UniProt-annotated variant site (in chocns)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDC42BPB p.Asp1234Asn Uncertain significance ★★ same condition
CDC42BPB p.Asp503Val Uncertain significance ★★ ⚠ same condition
CDC42BPB p.His1304Tyr Uncertain significance ★★ same condition
CDC42BPB p.Ser44Leu Uncertain significance ★★ ⚠ same condition
CDC42BPB p.Val52Ala Uncertain significance ★★ ⚠ same condition
CDC42BPB p.Ala1532Val Likely benign ★★ same condition
CDC42BPB p.Arg1570= Likely benign ★★ same condition
CDC42BPB p.Asn904Ser Benign/Likely benign ★★ 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-asp1069glu (accessed [today's date]).

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