Is BCL10 p.Tyr154= (c.462C>T) pathogenic?

BCL10 p.Tyr154= (c.462C>T) is classified Likely benign in BCL10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-06). Very rare (popmax 0.00169%, nfe); Associated with immunodeficiency 37.

What condition is associated with BCL10 p.Tyr154= (c.462C>T)?

BCL10 p.Tyr154= (c.462C>T) is associated with immunodeficiency 37 (ClinVar).

How common is BCL10 p.Tyr154= (c.462C>T) in the general population?

BCL10 p.Tyr154= (c.462C>T) is very rare (popmax 0.00169%, nfe) (gnomAD).

BCL10 p.Tyr154=

c.462C>T · VCV3652274

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00169%, nfe)

Conditions

immunodeficiency 37

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 3.9	GERP -0.5, phastCons 1
Overall
CADD	6.555	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00169% European (non-Finnish) · 20/1,179,992 alleles

Filtering AF 0.00111% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0009%

Overall 0.00137% 20/1,461,854 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: BCL10
Protein: p.Tyr154=
Coding: c.462C>T
MANE Select: NM_003921
Type: single nucleotide variant
Location: chr1:85267867 (GRCh38)
Gene constraint: LOEUF 0.637 · pLI 0.73 (gnomAD)
Structure: AlphaFold pLDDT 70.43 · 5 PDB

Full BCL10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency 37 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BCL10 p.Arg232Ter Uncertain significance ★★ same condition
BCL10 p.Arg87Gln Uncertain significance ★★ ⚠ same condition
BCL10 p.Cys119Tyr Uncertain significance ★★ ⚠ same condition
BCL10 p.Gln97Glu Uncertain significance ★★ ⚠ same condition
BCL10 p.Ile96Val Uncertain significance ★★ ⚠ same condition
BCL10 p.Leu177Ile Uncertain significance ★★ ⚠ same condition
BCL10 p.Thr162Met Uncertain significance ★★ ⚠ same condition
BCL10 p.Thr190Ala 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/bcl10-p-tyr154 (accessed [today's date]).

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