BCAS4

Summary

BCAS4 (breast carcinoma amplified sequence 4, HGNC:14367) is a protein-coding gene on chromosome 20q13.13, encoding Breast carcinoma-amplified sequence 4 (Q8TDM0).

Predicted to be located in cytoplasm. Predicted to be part of BLOC-1 complex.

Source: NCBI Gene 55653 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 52 total
• MANE Select transcript: NM_198799

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14367
Approved symbol	BCAS4
Name	breast carcinoma amplified sequence 4
Location	20q13.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20495, CNOL
Ensembl gene	ENSG00000124243
Ensembl biotype	protein_coding
OMIM	607471
Entrez	55653

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000358791, ENST00000371608, ENST00000445038, ENST00000463943, ENST00000485049, ENST00000609336, ENST00000912026, ENST00000912027, ENST00000912028, ENST00000912029, ENST00000912030, ENST00000912031, ENST00000912033

RefSeq mRNA: 3 — MANE Select: NM_198799 NM_001010974, NM_017843, NM_198799

CCDS: CCDS13432, CCDS33487

Canonical transcript exons

ENST00000371608 — 5 exons

Exon	Start	End
ENSE00001556559	50795061	50795173
ENSE00003477470	50830279	50830380
ENSE00003528368	50818211	50818282
ENSE00003608837	50876486	50877177
ENSE00003662327	50841766	50841900

Expression profiles

Bgee: expression breadth ubiquitous, 231 present calls, max score 86.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 83.4044 / max 1756.4253, expressed in 1515 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
185292	80.9146	1497
185290	1.4342	308
185289	0.5840	189
185291	0.4716	134

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	86.62	silver quality
lymph node	UBERON:0000029	85.19	gold quality
endothelial cell	CL:0000115	84.72	silver quality
prefrontal cortex	UBERON:0000451	83.72	gold quality
buccal mucosa cell	CL:0002336	83.39	gold quality
nucleus accumbens	UBERON:0001882	83.06	gold quality
anterior cingulate cortex	UBERON:0009835	83.04	gold quality
cingulate cortex	UBERON:0003027	82.91	gold quality
stromal cell of endometrium	CL:0002255	82.68	gold quality
pigmented layer of retina	UBERON:0001782	82.60	gold quality
vena cava	UBERON:0004087	82.53	silver quality
right frontal lobe	UBERON:0002810	82.37	gold quality
ventricular zone	UBERON:0003053	81.94	gold quality
neocortex	UBERON:0001950	81.53	gold quality
frontal cortex	UBERON:0001870	81.38	gold quality
granulocyte	CL:0000094	81.36	gold quality
Ammon’s horn	UBERON:0001954	81.20	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	81.12	gold quality
cerebral cortex	UBERON:0000956	80.54	gold quality
mucosa of stomach	UBERON:0001199	80.23	gold quality
middle temporal gyrus	UBERON:0002771	80.15	gold quality
lateral nuclear group of thalamus	UBERON:0002736	80.06	silver quality
telencephalon	UBERON:0001893	79.96	gold quality
caudate nucleus	UBERON:0001873	79.76	gold quality
tonsil	UBERON:0002372	79.45	gold quality
primary visual cortex	UBERON:0002436	79.37	gold quality
Brodmann (1909) area 9	UBERON:0013540	79.34	gold quality
ascending aorta	UBERON:0001496	79.28	gold quality
cortical plate	UBERON:0005343	79.22	gold quality
thoracic aorta	UBERON:0001515	79.19	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 7.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	191686.57
E-MTAB-7407	yes	88141.46
E-MTAB-9543	yes	11134.64
E-MTAB-9221	yes	787.30
E-ANND-3	yes	21.39
E-CURD-122	yes	18.08
E-GEOD-130148	yes	9.35
E-MTAB-8498	no	56.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting BCAS4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-3177-5P	99.65	70.38	1174
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309
HSA-MIR-519D-5P	99.41	69.30	2057
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-548AS-3P	99.12	69.12	2294
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-4638-3P	97.90	65.75	905

Literature-anchored findings (GeneRIF, showing 1)

• BCAS3 (17q23) and BCAS4 (20q13) undergo amplification, overexpression, and fusion in breast cancer. (PMID:12378525)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	Blos4	FBGN0036105

Paralogs (1): BLOC1S4 (ENSG00000186222)

Protein

Protein identifiers

Breast carcinoma-amplified sequence 4 — Q8TDM0 (reviewed: Q8TDM0)

All UniProt accessions (5): A0A0C4DGS6, A0A0C4DH49, A0A804CEY2, H7C4Y8, Q8TDM0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Brain, thymus, spleen, kidney and placenta. Overexpressed in most breast cancer cell lines.

Disease relevance. A chromosomal aberration involving BCAS4 has been found in some breast carcinoma cell lines. Translocation t(17;20)(q23;q13) with BCAS3.

Similarity. Belongs to the cappuccino family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8TDM0-1	1	yes
Q8TDM0-2	2
Q8TDM0-3	3

RefSeq proteins (3): NP_001010974, NP_060313, NP_942094* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024857	Cappuccino	Family

UniProt features (9 total): splice variant 4, sequence variant 2, chain 1, region of interest 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TDM0-F1	72.40	0.36

Functional residue map

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

Catalytic / active sites (1): 60–61 (breakpoint for translocation to form bcas4-bcas3)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): GCANCTGNY_MYOD_Q6, LIAO_METASTASIS, MODULE_95, GOCC_BLOC_1_COMPLEX, NUYTTEN_EZH2_TARGETS_DN, GOCC_BLOC_COMPLEX, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP, MODULE_49, LU_EZH2_TARGETS_UP, PEDRIOLI_MIR31_TARGETS_UP, MODULE_163, DCA_UP.V1_UP, CHAF1B_TARGET_GENES, DROSHA_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): cytoplasm (GO:0005737), BLOC-1 complex (GO:0031083)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
cellular anatomical structure	1
BLOC complex	1

Protein interactions and networks

STRING

588 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BCAS4	BCAS3	Q9H6U6	984
BCAS4	NUFIP1	Q9UHK0	544
BCAS4	ARFGEF2	Q9Y6D5	532
BCAS4	PSME3IP1	Q9GZU8	516
BCAS4	SULF2	Q8IWU5	476
BCAS4	ARMCX2	Q7L311	473
BCAS4	FXR2	P51116	472
BCAS4	ATP6V1E2	Q96A05	471
BCAS4	SHISA7	A6NL88	467
BCAS4	DDX55	Q8NHQ9	458
BCAS4	OR9K2	Q8NGE7	456
BCAS4	FAM209B	Q5JX69	450
BCAS4	FXR1	P51114	449
BCAS4	ATPAF1	Q5TC12	441
BCAS4	DIS3L2	Q8IYB7	418

IntAct

12 interactions, top by confidence:

A	B	Type	Score
DTNBP1	AP3B1	psi-mi:“MI:0914”(association)	0.350
BLOC1S1	LAMTOR5	psi-mi:“MI:0914”(association)	0.350
BLOC1S6	HSBP1	psi-mi:“MI:0914”(association)	0.350
BORCS7	SNAPIN	psi-mi:“MI:0914”(association)	0.350
BCAS4	SNAPIN	psi-mi:“MI:0914”(association)	0.350
BLOC1S6	KCNN4	psi-mi:“MI:0914”(association)	0.350
DTNBP1	DUSP14	psi-mi:“MI:0914”(association)	0.350
BLOC1S5	SRGAP2	psi-mi:“MI:0914”(association)	0.350
DTNBP1	SNAP23	psi-mi:“MI:0914”(association)	0.350

BioGRID (41): BCAS4 (Affinity Capture-MS), PKD2 (Affinity Capture-MS), BLOC1S6 (Affinity Capture-MS), BLOC1S2 (Affinity Capture-MS), BLOC1S5 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS), LOH12CR1 (Affinity Capture-MS), ATG4A (Affinity Capture-MS), SNAPIN (Affinity Capture-MS), BLOC1S3 (Affinity Capture-MS), SRCIN1 (Affinity Capture-MS), BCAS4 (Affinity Capture-MS), SRCIN1 (Affinity Capture-MS), BLOC1S5 (Affinity Capture-MS), BLOC1S6 (Affinity Capture-MS)

ESM2 similar proteins: A2AGX3, A2APT9, A3KFU9, O00221, O15040, O95170, P49796, P52734, P98174, Q27969, Q32KQ7, Q3TAA7, Q3UV31, Q5FW56, Q5QP82, Q5R866, Q5RA50, Q5RDC3, Q5T089, Q5VTJ3, Q5VUJ9, Q68UT4, Q69Z89, Q6AZ51, Q6PCP7, Q7Z5J1, Q80TL0, Q86V42, Q8BH06, Q8BL74, Q8BUM9, Q8C0R7, Q8N1F8, Q8NFT6, Q8R2K4, Q8TDM0, Q8VCC6, Q8WUA4, Q91WI7, Q969R8

Diamond homologs: A0A096LPI5, A6NIU2, A6NJG6, F2Z398, P0DTE4, P51957, Q09FC8, Q5H9K5, Q5T7P6, Q68CZ1, Q6B4Z3, Q6UX73, Q86U02, Q8IV13, Q8N7M2, Q8N9N2, Q8NDZ0, Q8NEM8, Q8TDM0, Q92918, Q96J02, Q96MD7, Q9BUA6, Q9NXG0, A7MB40, P78312, Q8CGI1, A2RRD8, A6NHJ4, P0CJ79, P17035, P51522, Q08AN1, Q0VGE8, Q3MIS6, Q5HY98, Q5R8X1, Q5RER9, Q5VIY5, Q6PDB4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 13 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
trans-Golgi Network Vesicle Budding	5	126.9×	1e-08
Golgi Associated Vesicle Biogenesis	5	100.2×	2e-08
Membrane Trafficking	5	18.5×	6e-05
Vesicle-mediated transport	5	17.4×	6e-05

GO biological processes:

GO term	Partners	Fold	FDR
anterograde synaptic vesicle transport	6	495.6×	6e-14
melanosome organization	6	324.1×	5e-13
anterograde axonal transport	6	290.6×	7e-13
neuron projection development	5	50.9×	8e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	8
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1627 predictions. Top by Δscore:

Variant	Effect	Δscore
20:50795170:CGAG:C	donor_loss	1.0000
20:50795171:GAGG:G	donor_loss	1.0000
20:50795172:AGGTA:A	donor_loss	1.0000
20:50795173:GGTAG:G	donor_loss	1.0000
20:50795174:GT:G	donor_loss	1.0000
20:50795175:T:A	donor_loss	1.0000
20:50818205:TTTCA:T	acceptor_loss	1.0000
20:50818207:TCAG:T	acceptor_loss	1.0000
20:50818208:CAGGC:C	acceptor_loss	1.0000
20:50818209:A:AG	acceptor_gain	1.0000
20:50818209:A:AT	acceptor_loss	1.0000
20:50818210:G:GA	acceptor_gain	1.0000
20:50830274:TGCA:T	acceptor_loss	1.0000
20:50830276:CA:C	acceptor_loss	1.0000
20:50830277:A:AG	acceptor_gain	1.0000
20:50830277:AGA:A	acceptor_loss	1.0000
20:50830278:G:GG	acceptor_gain	1.0000
20:50830278:GATC:G	acceptor_gain	1.0000
20:50830278:GATCA:G	acceptor_gain	1.0000
20:50830381:G:T	donor_loss	1.0000
20:50830382:T:G	donor_loss	1.0000
20:50841896:GGAAC:G	donor_gain	1.0000
20:50841897:GAAC:G	donor_gain	1.0000
20:50841897:GAACG:G	donor_gain	1.0000
20:50841898:A:T	donor_gain	1.0000
20:50841901:G:GG	donor_gain	1.0000
20:50876567:G:GT	donor_gain	1.0000
20:50876567:G:T	donor_gain	1.0000
20:50876631:A:T	donor_gain	1.0000
20:50876639:A:T	donor_gain	1.0000

AlphaMissense

1308 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:50818262:T:C	F78L	0.975
20:50818264:T:A	F78L	0.975
20:50818264:T:G	F78L	0.975
20:50841769:T:C	F120L	0.971
20:50841771:C:A	F120L	0.971
20:50841771:C:G	F120L	0.971
20:50841773:T:A	V121D	0.951
20:50818263:T:C	F78S	0.940
20:50830280:T:C	I85T	0.935
20:50830301:T:C	I92T	0.919
20:50841782:T:A	V124D	0.919
20:50830280:T:G	I85S	0.898
20:50830280:T:A	I85N	0.895
20:50818254:T:C	L75P	0.886
20:50841770:T:C	F120S	0.886
20:50830376:T:C	L117P	0.883
20:50818263:T:G	F78C	0.875
20:50818233:T:A	I68N	0.873
20:50841823:G:C	A138P	0.872
20:50818245:T:C	L72P	0.868
20:50795147:T:C	F52L	0.866
20:50795149:C:A	F52L	0.866
20:50795149:C:G	F52L	0.866
20:50841766:G:C	A119P	0.866
20:50830289:A:T	D88V	0.862
20:50830316:T:C	I97T	0.857
20:50830283:G:T	R86M	0.849
20:50830346:T:G	M107R	0.848
20:50830325:T:C	L100P	0.847
20:50841794:T:A	V128D	0.845

dbSNP variants (sampled 300 via entrez): RS1000045015 (20:50866676 G>C), RS1000045568 (20:50835642 A>C,G,T), RS1000064301 (20:50861025 T>C,G), RS1000076899 (20:50811336 G>T), RS1000100208 (20:50849973 TTAAAAA>T), RS1000147387 (20:50855595 G>T), RS1000181588 (20:50871744 G>A), RS1000191126 (20:50816080 C>G,T), RS1000192337 (20:50833260 G>A,T), RS1000245843 (20:50793698 T>C,G), RS1000257181 (20:50825022 C>T), RS1000268675 (20:50818872 C>A,T), RS1000302204 (20:50811735 G>T), RS1000303221 (20:50838169 G>A), RS1000311483 (20:50813435 G>A,C)

Disease associations

OMIM: gene MIM:607471 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST003487_3	Response to fenofibrate (total cholesterol levels)	7.000000e-06
GCST007637_54	Diffusing capacity of carbon monoxide	5.000000e-06
GCST008870_18	Keratinocyte cancer (MTAG)	2.000000e-13
GCST008871_1	Basal cell carcinoma	5.000000e-17
GCST90013410_70	Basal cell carcinoma	2.000000e-16

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007806	total cholesterol change measurement
EFO:0009369	diffusing capacity of the lung for carbon monoxide
EFO:0010176	keratinocyte carcinoma

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
Benzo(a)pyrene	affects methylation	2
Aflatoxin B1	increases methylation, affects methylation	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases expression	1
trichostatin A	affects expression	1
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acid	increases abundance, affects methylation	1
butyraldehyde	increases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
beta-methylcholine	affects expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
mesotrione	affects methylation, increases abundance	1
jinfukang	increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Atrazine	increases expression	1
Cannabinoids	affects methylation, increases abundance	1
Carbamazepine	affects expression	1
Cisplatin	affects response to substance	1
Cytarabine	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Fluorouracil	affects response to substance	1
Formaldehyde	increases expression	1

Clinical trials (associated diseases)

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