Is CBL p.Thr377Ala (c.1129A>G) pathogenic?

CBL p.Thr377Ala (c.1129A>G) is classified Uncertain significance in CBL (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-09-07). AlphaMissense: likely pathogenic (0.9937); Very rare (popmax 8.5e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CBL p.Thr377Ala (c.1129A>G)?

CBL p.Thr377Ala (c.1129A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CBL p.Thr377Ala (c.1129A>G) in the general population?

CBL p.Thr377Ala (c.1129A>G) is very rare (popmax 8.5e-05%, nfe) (gnomAD).

What do computational predictors say about CBL p.Thr377Ala (c.1129A>G)?

AlphaMissense predicts likely pathogenic (score 0.9937) — an in-silico prediction, not a clinical call.

CBL p.Thr377Ala

c.1129A>G · rs727502914 · VCV162832

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9937 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.5e-05%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9937	likely pathogenic
REVEL	0.824	moderately pathogenic-leaning
SaProt	LLR -13.85	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.1, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 22 kb · p 0.19 · regional, not allelic
Overall
CADD	27.4	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 8.5e-05% European (non-Finnish) · 1/1,176,868 alleles

Overall 6.86e-05% 1/1,458,364 alleles · very rare

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.Thr377Ala
Coding: c.1129A>G
MANE Select: NM_005188
dbSNP: rs727502914
Type: single nucleotide variant
Location: chr11:119278199 (GRCh38)
Gene constraint: LOEUF 0.622 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 64.27 · 34 PDB
Residue 377: the 'required for ubiquitination of spred2' region; an α-helix; the 'linker' region

Full CBL 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

CBL p.Thr377Ile Uncertain significance ★ ⚠ same residue
CBL p.Thr377Lys Uncertain significance ★ ⚠ same residue
CBL p.Thr377= Likely benign ★ same residue
CBL p.Lys389Thr Pathogenic/Likely pathogenic ★★ same condition
CBL p.Gln367Lys Conflicting classifications of pathogenicity ★ ⚠ same condition
CBL p.Thr377fs Uncertain significance ★ same residue
CBL p.Leu892fs Uncertain significance ★ same condition
CBL c.1096-1G>C Pathogenic/Likely pathogenic ★★ 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/cbl-p-thr377ala (accessed [today's date]).

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