Is CBL p.Ala11= (c.33C>T) pathogenic?

CBL p.Ala11= (c.33C>T) is classified Likely benign in CBL (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-20). Ultra-rare (popmax 0.047%, afr); Associated with RASopathy.

What condition is associated with CBL p.Ala11= (c.33C>T)?

CBL p.Ala11= (c.33C>T) is associated with RASopathy (ClinVar).

How common is CBL p.Ala11= (c.33C>T) in the general population?

CBL p.Ala11= (c.33C>T) is ultra-rare (popmax 0.047%, afr) (gnomAD).

CBL p.Ala11=

c.33C>T · rs760968593 · VCV1145334

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.047%, afr)

Conditions

RASopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.64	GERP -2.6, phastCons 0.007
Overall
CADD	11.85	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.047% African / African-American · 35/74,420 alleles

Filtering AF 0.0347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0305%

Overall 0.00253% 40/1,580,638 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.047%	2,126
Admixed American	0.00538%	18,602
Remaining individualsnot grpmax-eligible	0.00163%	61,286
European (non-Finnish)	8.56e-05%	1,167,925

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.Ala11=
Coding: c.33C>T
MANE Select: NM_005188
dbSNP: rs760968593
Type: single nucleotide variant
Location: chr11:119206450 (GRCh38)
Gene constraint: LOEUF 0.622 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 64.27 · 34 PDB
Residue 11: the 'sufficient for interaction with ephb1' region; the 'disordered' region

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

Disease context

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

Similar variants

CBL p.Ala11Asp Uncertain significance ★ ⚠ same residue
CBL p.Ala11Gly Uncertain significance ★ ⚠ same residue
CBL p.Ala11Ser Uncertain significance ★ ⚠ 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
CBL p.Arg420Leu 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-ala11 (accessed [today's date]).

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