Is CBL p.Asp460Gly (c.1379A>G) pathogenic?

CBL p.Asp460Gly (c.1379A>G) is classified Uncertain significance in CBL (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-11). AlphaMissense: ambiguous (0.3432); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with CBL p.Asp460Gly (c.1379A>G)?

CBL p.Asp460Gly (c.1379A>G) is associated with Cardiovascular phenotype (ClinVar).

How common is CBL p.Asp460Gly (c.1379A>G) in the general population?

CBL p.Asp460Gly (c.1379A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CBL p.Asp460Gly (c.1379A>G)?

AlphaMissense predicts ambiguous (score 0.3432) — an in-silico prediction, not a clinical call.

CBL p.Asp460Gly

c.1379A>G · VCV3485585

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3432 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.3432	ambiguous
REVEL	0.58	indeterminate
SaProt	LLR -7.89	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.3	GERP 2.1, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 22 kb · p 0.19 · regional, not allelic
Overall
CADD	27.1	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: CBL
Protein: p.Asp460Gly
Coding: c.1379A>G
MANE Select: NM_005188
Type: single nucleotide variant
Location: chr11:119278661 (GRCh38)
Gene constraint: LOEUF 0.622 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 64.27 · 34 PDB
Residue 460: the 'required for ubiquitination of spred2' region; the 'disordered' region

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CBL p.Asp460= Likely benign ★★ same residue
CBL p.Asp460dup Benign/Likely benign ★★ same residue
CBL p.Ala187Ser Uncertain significance ★★ ⚠ same condition
CBL p.Ala187Val Uncertain significance ★★ ⚠ same condition
CBL p.Ala208Thr Uncertain significance ★★ ⚠ same condition
CBL p.Ala385Gly Uncertain significance ★★ ⚠ same condition
CBL p.Ala450Val Uncertain significance ★★ ⚠ same condition
CBL p.Ala513Thr Uncertain significance ★★ ⚠ 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/cbl-p-asp460gly (accessed [today's date]).

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