Is BCL10 p.Arg232Ter (c.694C>T) pathogenic?

BCL10 p.Arg232Ter (c.694C>T) is classified Uncertain significance in BCL10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-03-18). Very rare (popmax 0.00585%, amr); Associated with malignant mesothelioma.

What condition is associated with BCL10 p.Arg232Ter (c.694C>T)?

BCL10 p.Arg232Ter (c.694C>T) is associated with malignant mesothelioma, MALT lymphoma, testicular germ cell tumor (ClinVar).

How common is BCL10 p.Arg232Ter (c.694C>T) in the general population?

BCL10 p.Arg232Ter (c.694C>T) is very rare (popmax 0.00585%, amr) (gnomAD).

How is Pleural mesothelioma inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

BCL10 p.Arg232Ter

c.694C>T · rs376302558 · VCV652565

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00585%, amr)

Conditions

malignant mesothelioma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.4	GERP 0.37, phastCons 0.91
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00585% Admixed American · 3/51,310 alleles

Filtering AF 0.00311% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00279%

Overall 0.00374% 59/1,578,962 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00585%	17,103
South Asian	0.00584%	17,124
African / African-American	0.0041%	24,361
European (non-Finnish)	0.00403%	24,797
Remaining individualsnot grpmax-eligible	0.00164%	60,870

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.Arg232Ter
Coding: c.694C>T
MANE Select: NM_003921
dbSNP: rs376302558
Type: single nucleotide variant
Location: chr1:85267635 (GRCh38)
Gene constraint: LOEUF 0.637 · pLI 0.73 (gnomAD)
Structure: AlphaFold pLDDT 70.43 · 5 PDB
Residue 232: the 'disordered' region

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

Disease context

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

Also linked: MALT lymphoma testicular germ cell tumor lymphoma, non-Hodgkin, familial immunodeficiency 37

For Pleural mesothelioma (Orphanet):

Inheritance: Not applicable
Onset: All ages
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

BCL10 p.Arg232Gln Uncertain significance ★ ⚠ same residue
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-arg232ter (accessed [today's date]).

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