Is BCL10 p.Pro6Gln (c.17C>A) pathogenic?

BCL10 p.Pro6Gln (c.17C>A) is classified Uncertain significance in BCL10 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-17). AlphaMissense: likely benign (0.1094); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with BCL10 p.Pro6Gln (c.17C>A)?

BCL10 p.Pro6Gln (c.17C>A) is associated with Inborn genetic diseases (ClinVar).

How common is BCL10 p.Pro6Gln (c.17C>A) in the general population?

BCL10 p.Pro6Gln (c.17C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BCL10 p.Pro6Gln (c.17C>A)?

AlphaMissense predicts likely benign (score 0.1094) — an in-silico prediction, not a clinical call.

BCL10 p.Pro6Gln

c.17C>A · VCV4201026

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1094 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1094	likely benign
REVEL	0.044	moderately benign-leaning
SaProt	LLR -6.92	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.006	GERP -4.4
Regional constraint	o/e 1.45	unconstrained · MANE · 39 bp · p 0.067 · regional, not allelic
Overall
CADD	19.69	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BCL10
Protein: p.Pro6Gln
Coding: c.17C>A
MANE Select: NM_003921
Type: single nucleotide variant
Location: chr1:85276336 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BCL10 p.Cys119Tyr Uncertain significance ★★ ⚠ same condition
BCL10 p.Ile96Val Uncertain significance ★★ ⚠ same condition
BCL10 p.Leu177Ile Uncertain significance ★★ ⚠ same condition
BCL10 p.Pro6fs Pathogenic ★ same residue
BCL10 p.Glu10Ala Uncertain significance ★ ⚠ same condition
BCL10 p.Lys115Gln Uncertain significance ★ ⚠ same condition
BCL10 p.Thr214Ala Uncertain significance ★ ⚠ same condition
BCL10 p.Thr52Ile 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-pro6gln (accessed [today's date]).

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