BCL7B

Chr 7

BAF chromatin remodeling complex subunit BCL7B

Also known as: SMARCJ2

NCBI Gene: 9275 ENSG00000106635 UniProt: Q9BQE9 OMIM: 605846

The protein encoded by this gene positively regulates apoptosis, negatively regulates Wnt signaling components CTNNB1 and HMGA1, and is involved in cell cycle progression and stem cell differentiation. BCL7B is located in a chromosomal region commonly deleted in Williams syndrome, though specific disease associations with isolated BCL7B mutations are not well-established in the provided data. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.714).

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a member of the BCL7 family including BCL7A, BCL7B and BCL7C proteins. This member is BCL7B, which contains a region that is highly similar to the N-terminal segment of BCL7A or BCL7C proteins. The BCL7A protein is encoded by the gene known to be directly involved in a three-way gene translocation in a Burkitt lymphoma cell line. This gene is located at a chromosomal region commonly deleted in Williams syndrome. This gene is highly conserved from C. elegans to human. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2010]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 0.71

Clinical Summary— BCL7B

⚡

Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.28) despite low pLI — interpret in context.

📋

ClinVar Variants

16 VUS of 31 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.71LOEUF

pLI 0.185

Z-score 2.21

OE 0.28 (0.13–0.71)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.22Z-score

OE missense 0.68 (0.56–0.82)

77 obs / 113.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.28 (0.13–0.71)

0≤0.351.4

Missense OE?0.68 (0.56–0.82)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 3 / 10.9Missense obs/exp: 77 / 113.5Syn Z: 0.01

This gene — mechanism propensity

0.6648th %ile

GOF

0.5071th %ile

LOF

0.4430th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

31 submitted variants in ClinVar

ClinVar

Classification Summary

VUS16

Likely Benign3

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	16	0	16
Likely Benign	1	2	3
Benign	0	0	0
Total	17	2	19

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

163 pathogenic / likely-pathogenic (of 168) ClinVar copy-number / structural variants overlap BCL7B — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →