Is CDC42BPB p.Asp503Val (c.1508A>T) pathogenic?

CDC42BPB p.Asp503Val (c.1508A>T) is classified Uncertain significance in CDC42BPB (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-14). AlphaMissense: likely benign (0.1561); Very rare (popmax 0.00503%, amr); Associated with Inborn genetic diseases.

What condition is associated with CDC42BPB p.Asp503Val (c.1508A>T)?

CDC42BPB p.Asp503Val (c.1508A>T) is associated with Inborn genetic diseases (ClinVar).

How common is CDC42BPB p.Asp503Val (c.1508A>T) in the general population?

CDC42BPB p.Asp503Val (c.1508A>T) is very rare (popmax 0.00503%, amr) (gnomAD).

What do computational predictors say about CDC42BPB p.Asp503Val (c.1508A>T)?

AlphaMissense predicts likely benign (score 0.1561) — an in-silico prediction, not a clinical call.

CDC42BPB p.Asp503Val

c.1508A>T · VCV3829794

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1561 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00503%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1561	likely benign
REVEL	0.42	indeterminate
SaProt	LLR -7.22	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 2.4, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 8,980 bp · p 0.023 · regional, not allelic
Overall
CADD	22.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00503% Admixed American · 3/59,688 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00067%

Overall 0.00031% 5/1,613,134 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00503%	19,896
Remaining individualsnot grpmax-eligible	0.0032%	31,225

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.Asp503Val
Coding: c.1508A>T
MANE Select: NM_006035
Type: single nucleotide variant
Location: chr14:102974149 (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

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.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
CDC42BPB p.Leu1262Phe 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-asp503val (accessed [today's date]).

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