Is CBL p.Arg563Cys (c.1687C>T) pathogenic?

CBL p.Arg563Cys (c.1687C>T) is classified Uncertain significance in CBL (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-04-01). AlphaMissense: likely pathogenic (0.5801); Ultra-rare (popmax 0.0164%, mid); Associated with Noonan syndrome and Noonan-related syndrome.

What condition is associated with CBL p.Arg563Cys (c.1687C>T)?

CBL p.Arg563Cys (c.1687C>T) is associated with Noonan syndrome and Noonan-related syndrome, RASopathy (ClinVar).

How common is CBL p.Arg563Cys (c.1687C>T) in the general population?

CBL p.Arg563Cys (c.1687C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about CBL p.Arg563Cys (c.1687C>T)?

AlphaMissense predicts likely pathogenic (score 0.5801) — an in-silico prediction, not a clinical call.

CBL p.Arg563Cys

c.1687C>T · rs768837912 · VCV1334233

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.5801 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Noonan syndrome and Noonan-related syndrome

Computational evidence

Protein change
AlphaMissense	0.5801	likely pathogenic
REVEL	0.43	indeterminate
SaProt	LLR -10.84	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 22 kb · p 0.19 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.000803% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00065%

Overall 0.00112% 18/1,614,052 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
European (non-Finnish)	0.00136%	73,752
South Asian	0.0011%	91,086

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: CBL
Protein: p.Arg563Cys
Coding: c.1687C>T
MANE Select: NM_005188
dbSNP: rs768837912
Type: single nucleotide variant
Location: chr11:119285312 (GRCh38)
Gene constraint: LOEUF 0.622 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 64.27 · 34 PDB
Residue 563: 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

Noonan syndrome and Noonan-related syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: RASopathy

Similar variants

CBL p.Arg563His Uncertain significance ★★ ⚠ same residue
CBL p.Arg563Leu Uncertain significance ★ ⚠ same residue
CBL p.Arg563Pro Uncertain significance ★ ⚠ same residue
CBL p.Arg563= Likely benign ★ same residue
CBL c.1096-1G>C Pathogenic/Likely pathogenic ★★ same condition
CBL c.1096-1G>T Pathogenic ★★ same condition
CBL c.1228-2A>G Pathogenic/Likely pathogenic ★★ same condition
CBL p.Arg420Gln Pathogenic/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/cbl-p-arg563cys (accessed [today's date]).

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