BCL7C

Summary

BCL7C (BAF chromatin remodeling complex subunit BCL7C, HGNC:1006) is a protein-coding gene on chromosome 16p11.2, encoding B-cell CLL/lymphoma 7 protein family member C (Q8WUZ0). May play an anti-apoptotic role.

This gene is identified by the similarity of its product to the N-terminal region of BCL7A protein. 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. The function of this gene has not yet been determined. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 9274 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 40 total
• MANE Select transcript: NM_004765

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1006
Approved symbol	BCL7C
Name	BAF chromatin remodeling complex subunit BCL7C
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Aliases	SMARCJ3
Ensembl gene	ENSG00000099385
Ensembl biotype	protein_coding
OMIM	605847
Entrez	9274

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000215115, ENST00000380317, ENST00000572628, ENST00000574418, ENST00000576194, ENST00000936619, ENST00000947224, ENST00000947225

RefSeq mRNA: 2 — MANE Select: NM_004765 NM_001286526, NM_004765

CCDS: CCDS10693, CCDS67012

Canonical transcript exons

ENST00000215115 — 6 exons

Exon	Start	End
ENSE00000648530	30892586	30892747
ENSE00000648531	30892840	30892948
ENSE00000648532	30893212	30893290
ENSE00001148672	30887795	30887990
ENSE00002656701	30893853	30894077
ENSE00003524175	30888860	30888945

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 96.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.4355 / max 127.9912, expressed in 1815 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157099	22.5163	1815
157100	1.2225	789
157098	0.5287	331
157093	0.1056	57
157101	0.0624	10

Top tissues by expression

286 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	96.34	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	95.96	gold quality
apex of heart	UBERON:0002098	95.65	gold quality
endocervix	UBERON:0000458	95.39	gold quality
ectocervix	UBERON:0012249	95.03	gold quality
popliteal artery	UBERON:0002250	95.02	gold quality
tibial artery	UBERON:0007610	95.02	gold quality
granulocyte	CL:0000094	94.98	gold quality
right coronary artery	UBERON:0001625	94.84	gold quality
aorta	UBERON:0000947	94.81	gold quality
ascending aorta	UBERON:0001496	94.66	gold quality
thoracic aorta	UBERON:0001515	94.66	gold quality
olfactory bulb	UBERON:0002264	94.61	gold quality
left uterine tube	UBERON:0001303	94.48	gold quality
left coronary artery	UBERON:0001626	94.42	gold quality
left ovary	UBERON:0002119	94.42	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.40	gold quality
coronary artery	UBERON:0001621	94.29	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.27	gold quality
right ovary	UBERON:0002118	94.24	gold quality
descending thoracic aorta	UBERON:0002345	94.12	gold quality
metanephros cortex	UBERON:0010533	94.09	gold quality
skin of leg	UBERON:0001511	94.07	gold quality
body of uterus	UBERON:0009853	93.95	gold quality
lower esophagus	UBERON:0013473	93.84	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.82	gold quality
skin of abdomen	UBERON:0001416	93.81	gold quality
nerve	UBERON:0001021	93.34	gold quality
tibial nerve	UBERON:0001323	93.34	gold quality
mucosa of transverse colon	UBERON:0004991	93.10	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-HCAD-13	yes	26.92
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• BCL7C suppresses ovarian cancer growth by inactivating mutant p53. (PMID:33306126)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Bcl7c	ENSMUSG00000030814
rattus_norvegicus	Bcl7c	ENSRNOG00000018916
drosophila_melanogaster	BCL7-like	FBGN0026149
caenorhabditis_elegans		WBGENE00016192

Paralogs (2): BCL7B (ENSG00000106635), BCL7A (ENSG00000110987)

Protein

Protein identifiers

B-cell CLL/lymphoma 7 protein family member C — Q8WUZ0 (reviewed: Q8WUZ0)

All UniProt accessions (3): Q8WUZ0, I3L1Q2, I3L4D5

UniProt curated annotations — full annotation on UniProt →

Function. May play an anti-apoptotic role.

Tissue specificity. Ubiquitous.

Similarity. Belongs to the BCL7 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WUZ0-1	1	yes
Q8WUZ0-2	2

RefSeq proteins (2): NP_001273455, NP_004756* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006804	BCL7	Family

Pfam: PF04714

UniProt features (16 total): modified residue 9, sequence conflict 2, compositionally biased region 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WUZ0-F1	63.71	0.18

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (9): 122, 126, 156, 97, 100, 103, 111, 114, 118

Function

Pathways and Gene Ontology

Reactome pathways

13 pathways

ID	Pathway
R-HSA-9824585	Regulation of MITF-M-dependent genes involved in pigmentation
R-HSA-9845323	Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs)
R-HSA-9933937	Formation of the canonical BAF (cBAF) complex
R-HSA-9933939	Formation of the polybromo-BAF (pBAF) complex
R-HSA-9933946	Formation of the embryonic stem cell BAF (esBAF) complex
R-HSA-9933947	Formation of the non-canonical BAF (ncBAF) complex
R-HSA-9934037	Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)
R-HSA-1266738	Developmental Biology
R-HSA-212165	Epigenetic regulation of gene expression
R-HSA-74160	Gene expression (Transcription)
R-HSA-9730414	MITF-M-regulated melanocyte development
R-HSA-9842860	Regulation of endogenous retroelements
R-HSA-9856651	MITF-M-dependent gene expression

MSigDB gene sets: 162 (showing top): GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, RNGTGGGC_UNKNOWN, GOBP_CHROMOSOME_ORGANIZATION, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_REGULATION_OF_DNA_REPAIR, SP1_Q2_01, GOBP_NUCLEOTIDE_EXCISION_REPAIR, GOBP_REGULATION_OF_CHROMOSOME_SEGREGATION, MYCMAX_01, chr16p11, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_REGULATION_OF_CELL_CYCLE_G1_S_PHASE_TRANSITION, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_CELL_CYCLE_G1_S_PHASE_TRANSITION

GO Biological Process (11): chromatin remodeling (GO:0006338), regulation of transcription by RNA polymerase II (GO:0006357), apoptotic process (GO:0006915), positive regulation of cell population proliferation (GO:0008284), regulation of mitotic metaphase/anaphase transition (GO:0030071), negative regulation of cell differentiation (GO:0045596), regulation of G0 to G1 transition (GO:0070316), positive regulation of stem cell population maintenance (GO:1902459), regulation of G1/S transition of mitotic cell cycle (GO:2000045), positive regulation of double-strand break repair (GO:2000781), regulation of nucleotide-excision repair (GO:2000819)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): chromatin (GO:0000785), nucleoplasm (GO:0005654), SWI/SNF complex (GO:0016514), GBAF complex (GO:0140288)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
SWI/SNF chromatin remodelers	5
MITF-M-dependent gene expression	1
Regulation of endogenous retroelements	1
Gene expression (Transcription)	1
Developmental Biology	1
Epigenetic regulation of gene expression	1
MITF-M-regulated melanocyte development	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of mitotic cell cycle phase transition	2
cellular anatomical structure	2
SWI/SNF superfamily-type complex	2
chromatin organization	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
metaphase/anaphase transition of mitotic cell cycle	1
regulation of metaphase/anaphase transition of cell cycle	1
cell differentiation	1
regulation of cell differentiation	1
negative regulation of cellular process	1
negative regulation of developmental process	1
regulation of cell cycle process	1
G0 to G1 transition	1
stem cell population maintenance	1
positive regulation of developmental process	1
positive regulation of multicellular organismal process	1
regulation of stem cell population maintenance	1
G1/S transition of mitotic cell cycle	1
regulation of cell cycle G1/S phase transition	1
double-strand break repair	1
positive regulation of DNA repair	1
regulation of double-strand break repair	1
regulation of DNA repair	1
nucleotide-excision repair	1
binding	1
chromosome	1
nuclear lumen	1

Protein interactions and networks

STRING

516 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BCL7C	CALD1	Q05682	779
BCL7C	DPF1	Q92782	751
BCL7C	DPF2	Q92785	730
BCL7C	BCL7B	Q9BQE9	716
BCL7C	BRD9	Q9H8M2	706
BCL7C	ARID1A	O14497	678
BCL7C	PHF10	Q8WUB8	676
BCL7C	SMARCC1	Q92922	673
BCL7C	BICRAL	Q6AI39	670
BCL7C	SMARCD1	Q96GM5	666
BCL7C	SMARCA4	P51532	640
BCL7C	BRD7	Q9NPI1	609
BCL7C	SMARCA2	P51531	598
BCL7C	SS18L1	O75177	579
BCL7C	BCL7A	Q4VC05	544

IntAct

74 interactions, top by confidence:

A	B	Type	Score
SMARCB1	ARID1A	psi-mi:“MI:0914”(association)	0.860
SMARCE1	ARID1A	psi-mi:“MI:0914”(association)	0.840
SMARCD1	ARID1A	psi-mi:“MI:0914”(association)	0.790
SMARCC2	ARID1A	psi-mi:“MI:0914”(association)	0.790
DPF2	ARID1A	psi-mi:“MI:0914”(association)	0.730
SMARCE1	SMARCA2	psi-mi:“MI:0914”(association)	0.730
NFIC	NFIB	psi-mi:“MI:2364”(proximity)	0.690
BCL7C	ARID1A	psi-mi:“MI:0914”(association)	0.640
BCL7A	ARID1A	psi-mi:“MI:0914”(association)	0.640
BCL7C	SCIN	psi-mi:“MI:0915”(physical association)	0.560
G3BP1	COX5A	psi-mi:“MI:0914”(association)	0.530
ARID1A	ACTL6A	psi-mi:“MI:0914”(association)	0.530
DPF3	ARID1A	psi-mi:“MI:0914”(association)	0.530
PHACTR2	ACTA2	psi-mi:“MI:0914”(association)	0.530
FOS	MYO1C	psi-mi:“MI:2364”(proximity)	0.480
Csnk1d	WWP2	psi-mi:“MI:0914”(association)	0.350
ATXN3	HLA-A	psi-mi:“MI:0914”(association)	0.350
NEIL3	SF3B2	psi-mi:“MI:0914”(association)	0.350
SPRTN	RALGAPA2	psi-mi:“MI:0914”(association)	0.350

BioGRID (238): BCL7C (Affinity Capture-MS), BCL7C (Affinity Capture-MS), BCL7C (Affinity Capture-MS), BCL7C (Affinity Capture-MS), ARID1A (Co-fractionation), BCL7C (Co-fractionation), BCL7C (Co-fractionation), BCL7C (Co-fractionation), BCL7C (Co-fractionation), BCL7C (Co-fractionation), DPF2 (Co-fractionation), SMARCA4 (Co-fractionation), SMARCB1 (Co-fractionation), SMARCC1 (Co-fractionation), SMARCC2 (Co-fractionation)

ESM2 similar proteins: A0A0U1RQG5, A1L429, A6NDE8, A6NER3, A6NGK3, E1AZ71, O08664, O60829, O75459, O76087, P0C2W7, P0CL80, P0CL81, P0CL82, P0DSO3, P0DTW1, P52651, P62521, P86478, P86479, P86480, P86481, P86496, Q13066, Q13069, Q13070, Q17QW4, Q28181, Q2T9P9, Q32PA2, Q4V321, Q4V326, Q5JQC4, Q5U2Y8, Q62100, Q63803, Q64256, Q6NT46, Q6X7S9, Q7Z2X7

Diamond homologs: A2BIL8, O08664, Q09242, Q3T0A6, Q4VC05, Q5XFY4, Q5XH61, Q6DEV7, Q6NWJ0, Q8WUZ0, Q921K9, Q9BQE9, Q9CXE2

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
BCL7C	“form complex”	GBAF	binding
BCL7C	“form complex”	“Embryonic stem cell-specific SWI/SNF”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 83 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Formation of the canonical BAF (cBAF) complex	11	104.2×	6e-19
Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)	12	81.8×	6e-19
Formation of the embryonic stem cell BAF (esBAF) complex	9	80.7×	4e-14
Formation of the polybromo-BAF (pBAF) complex	8	75.8×	2e-12
Formation of the non-canonical BAF (ncBAF) complex	6	60.2×	1e-08
Regulation of endogenous retroelements	10	55.0×	7e-14
Regulation of MITF-M-dependent genes involved in pigmentation	12	47.6×	9e-16
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known	8	35.9×	1e-09

GO biological processes:

GO term	Partners	Fold	FDR
regulation of G0 to G1 transition	12	102.4×	1e-19
regulation of nucleotide-excision repair	13	99.0×	6e-21
regulation of mitotic metaphase/anaphase transition	12	75.3×	7e-18
positive regulation of T cell differentiation	10	57.6×	8e-14
positive regulation of double-strand break repair	12	52.2×	6e-16
positive regulation of myoblast differentiation	11	51.0×	2e-14
nucleosome disassembly	5	50.8×	2e-06
regulation of G1/S transition of mitotic cell cycle	12	46.5×	2e-15

Disease & clinical

Clinical variants and AI predictions

ClinVar

40 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	31
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

753 predictions. Top by Δscore:

Variant	Effect	Δscore
16:30888854:TCTCA:T	donor_loss	1.0000
16:30888855:CTCAC:C	donor_loss	1.0000
16:30888856:TCA:T	donor_loss	1.0000
16:30888857:CA:C	donor_loss	1.0000
16:30888858:A:AT	donor_loss	1.0000
16:30888859:C:CG	donor_loss	1.0000
16:30893287:CTCC:C	acceptor_gain	1.0000
16:30893288:TCCC:T	acceptor_loss	1.0000
16:30893289:CC:C	acceptor_gain	1.0000
16:30893290:CC:C	acceptor_gain	1.0000
16:30893290:CCTG:C	acceptor_loss	1.0000
16:30893291:C:CC	acceptor_gain	1.0000
16:30893292:T:A	acceptor_loss	1.0000
16:30888858:A:AC	donor_gain	0.9900
16:30888859:C:CC	donor_gain	0.9900
16:30888859:CCT:C	donor_gain	0.9900
16:30888943:GATCT:G	acceptor_loss	0.9900
16:30888944:ATCTG:A	acceptor_loss	0.9900
16:30888946:C:A	acceptor_loss	0.9900
16:30888946:C:CC	acceptor_gain	0.9900
16:30888947:T:A	acceptor_loss	0.9900
16:30888952:C:CT	acceptor_gain	0.9900
16:30892838:A:AC	donor_gain	0.9900
16:30892839:C:CC	donor_gain	0.9900
16:30892947:TCCTG:T	acceptor_loss	0.9900
16:30892948:CCTGG:C	acceptor_loss	0.9900
16:30892949:C:CC	acceptor_gain	0.9900
16:30892950:T:A	acceptor_loss	0.9900
16:30893210:ACCT:A	donor_gain	0.9900
16:30893211:C:CT	donor_loss	0.9900

AlphaMissense

1381 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:30893239:C:A	W48C	1.000
16:30893239:C:G	W48C	1.000
16:30893240:C:G	W48S	1.000
16:30893241:A:G	W48R	1.000
16:30893241:A:T	W48R	1.000
16:30893242:C:A	K47N	1.000
16:30893242:C:G	K47N	1.000
16:30893244:T:C	K47E	1.000
16:30893249:A:C	I45S	1.000
16:30893249:A:G	I45T	1.000
16:30893249:A:T	I45N	1.000
16:30893255:A:G	L43P	1.000
16:30893255:A:T	L43H	1.000
16:30893278:C:A	W35C	1.000
16:30893278:C:G	W35C	1.000
16:30893279:C:G	W35S	1.000
16:30893280:A:G	W35R	1.000
16:30893280:A:T	W35R	1.000
16:30893284:C:A	K33N	1.000
16:30893284:C:G	K33N	1.000
16:30893290:C:A	W31C	1.000
16:30893290:C:G	W31C	1.000
16:30893853:C:G	W31S	1.000
16:30893854:A:G	W31R	1.000
16:30893854:A:T	W31R	1.000
16:30893871:A:T	I25N	1.000
16:30893878:C:G	A23P	1.000
16:30893888:C:A	K19N	1.000
16:30893888:C:G	K19N	1.000
16:30893900:C:A	K15N	1.000

dbSNP variants (sampled 300 via entrez): RS1000000851 (16:30894082 C>A), RS1000012560 (16:30833590 G>T), RS1000095980 (16:30880730 G>A), RS1000096903 (16:30894283 A>G,T), RS1000132489 (16:30873490 C>G,T), RS1000140225 (16:30864792 T>G), RS1000200395 (16:30874756 C>G), RS1000208268 (16:30874088 C>A,T), RS1000287759 (16:30840653 C>A,T), RS1000355640 (16:30867949 C>G,T), RS1000360676 (16:30866704 A>G), RS1000447847 (16:30880433 C>T), RS1000512447 (16:30842180 T>C), RS1000551303 (16:30889043 G>A), RS1000661776 (16:30846162 A>C)

Disease associations

OMIM: gene MIM:605847 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST004028_8	Immunoglobulin light chain (AL) amyloidosis	4.000000e-06
GCST005276_4	Dementia with Lewy bodies	1.000000e-08
GCST007931_50	Medication use (HMG CoA reductase inhibitors)	2.000000e-09
GCST010989_9	Body size at age 10	2.000000e-12

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009932	HMG CoA reductase inhibitor use measurement
EFO:0009819	comparative body size at age 10, self-reported

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, increases methylation	2
aristolochic acid I	increases expression	1
FR900359	affects phosphorylation	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	increases methylation	1
coumarin	decreases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
monomethylarsonous acid	decreases expression	1
K 7174	decreases expression	1
abrine	decreases expression	1
(+)-JQ1 compound	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Sunitinib	decreases expression	1
Caffeine	affects phosphorylation	1
Cisplatin	increases expression	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Potassium Dichromate	increases expression	1
Theophylline	affects cotreatment, decreases expression	1
Thiram	decreases expression	1
Valproic Acid	decreases expression, increases methylation	1
Cyclosporine	decreases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.