Is CDC42BPG p.Phe1410Val (c.4228T>G) pathogenic?

CDC42BPG p.Phe1410Val (c.4228T>G) is classified Uncertain significance in CDC42BPG (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-25). AlphaMissense: ambiguous (0.5373); Absent from gnomAD v4.1.

How common is CDC42BPG p.Phe1410Val (c.4228T>G) in the general population?

CDC42BPG p.Phe1410Val (c.4228T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDC42BPG p.Phe1410Val (c.4228T>G)?

AlphaMissense predicts ambiguous (score 0.5373) — an in-silico prediction, not a clinical call.

CDC42BPG p.Phe1410Val

c.4228T>G · rs2497392421 · VCV2478949

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5373 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.5373	ambiguous
REVEL	0.56	indeterminate
SaProt	LLR -5.72	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8	GERP 1.6, phastCons 1
Regional constraint	o/e 1.21	unconstrained · MANE · 3,214 bp · p 0.00049 · regional, not allelic
Overall
CADD	22.9	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CDC42BPG
Protein: p.Phe1410Val
Coding: c.4228T>G
MANE Select: NM_017525
dbSNP: rs2497392421
Type: single nucleotide variant
Location: chr11:64827321 (GRCh38)
Gene constraint: LOEUF 1.039 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.90

Full CDC42BPG gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDC42BPG p.Ile77= Benign ★★ same type
CDC42BPG p.Lys467Asn Benign ★★ same type
CDC42BPG p.Pro1257= Benign ★★ same type
CDC42BPG p.Ala1013Val Uncertain significance ★ ⚠ same type
CDC42BPG p.Ala1036Val Uncertain significance ★ ⚠ same type
CDC42BPG p.Ala1071Val Uncertain significance ★ ⚠ same type
CDC42BPG p.Ala1098Thr Uncertain significance ★ ⚠ same type
CDC42BPG p.Ala1242Val 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/cdc42bpg-p-phe1410val (accessed [today's date]).

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