BRMS1L

Summary

BRMS1L (BRMS1 like transcriptional repressor, HGNC:20512) is a protein-coding gene on chromosome 14q13.2, encoding Breast cancer metastasis-suppressor 1-like protein (Q5PSV4). Involved in the histone deacetylase (HDAC1)-dependent transcriptional repression activity.

The protein encoded by this gene shows sequence similarity to the human breast carcinoma metastasis suppressor (BRMS1) protein and the mammalian Sds3 (suppressor of defective silencing 3) proteins. This protein is a component of the mSin3a family of histone deacetylase complexes (HDAC).

Source: NCBI Gene 84312 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 41 total — 5 pathogenic
• MANE Select transcript: NM_032352

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20512
Approved symbol	BRMS1L
Name	BRMS1 like transcriptional repressor
Location	14q13.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC11296, FLJ39177, p40
Ensembl gene	ENSG00000100916
Ensembl biotype	protein_coding
OMIM	618514
Entrez	84312

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000216807, ENST00000547420, ENST00000548758, ENST00000551774, ENST00000552677, ENST00000552849, ENST00000876807, ENST00000876808

RefSeq mRNA: 1 — MANE Select: NM_032352 NM_032352

CCDS: CCDS32066

Canonical transcript exons

ENST00000216807 — 10 exons

Exon	Start	End
ENSE00001280291	35870360	35871963
ENSE00002386914	35826338	35826658
ENSE00003481619	35865722	35865761
ENSE00003490474	35832978	35833105
ENSE00003592426	35834844	35834923
ENSE00003616044	35831410	35831500
ENSE00003631359	35863870	35863953
ENSE00003652581	35864935	35864999
ENSE00003677012	35862590	35862686
ENSE00003682139	35867906	35868032

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 96.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.1341 / max 157.5000, expressed in 1825 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120793	24.1341	1825
139262	3.4721	1428
139261	2.4437	1146
139264	2.0007	850
139263	0.9156	580

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	96.02	gold quality
cardiac muscle of right atrium	UBERON:0003379	95.88	gold quality
Brodmann (1909) area 46	UBERON:0006483	94.73	gold quality
deltoid	UBERON:0001476	94.28	gold quality
myocardium	UBERON:0002349	94.00	gold quality
tibialis anterior	UBERON:0001385	92.92	gold quality
vastus lateralis	UBERON:0001379	92.65	gold quality
biceps brachii	UBERON:0001507	92.33	gold quality
quadriceps femoris	UBERON:0001377	91.98	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	91.59	gold quality
epithelial cell of pancreas	CL:0000083	91.49	gold quality
heart right ventricle	UBERON:0002080	91.32	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	90.83	gold quality
entorhinal cortex	UBERON:0002728	90.58	gold quality
superior frontal gyrus	UBERON:0002661	90.17	gold quality
Brodmann (1909) area 23	UBERON:0013554	90.10	gold quality
lateral nuclear group of thalamus	UBERON:0002736	89.92	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.71	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.68	gold quality
postcentral gyrus	UBERON:0002581	89.63	gold quality
skeletal muscle tissue	UBERON:0001134	89.56	gold quality
kidney epithelium	UBERON:0004819	89.24	silver quality
muscle tissue	UBERON:0002385	89.14	gold quality
parietal lobe	UBERON:0001872	88.87	gold quality
middle temporal gyrus	UBERON:0002771	88.86	gold quality
pons	UBERON:0000988	87.85	gold quality
prefrontal cortex	UBERON:0000451	87.35	gold quality
endothelial cell	CL:0000115	86.69	gold quality
dorsal plus ventral thalamus	UBERON:0001897	86.69	gold quality
pigmented layer of retina	UBERON:0001782	86.57	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.13
E-MTAB-6379	no	602.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

134 targeting BRMS1L, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-141-3P	99.94	72.79	2421

Literature-anchored findings (GeneRIF, showing 2)

• low levels of BRMS1L is associated with glioma progression and plays as an independent poor prognosis biomarker. The up-regulation of BRMS1L suppresses glioma cells’ invasion. All of those indicate that BRMS1L is a novel prognostic biomarker with potential anti-invasion therapeutic implications in GBM. (PMID:29660900)
• BRMS1L suppresses ovarian cancer metastasis via inhibition of the beta-catenin-WNT pathway. (PMID:30118697)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	brms1	ENSDARG00000051955
mus_musculus	Brms1l	ENSMUSG00000012076
rattus_norvegicus	Brms1l	ENSRNOG00000008249
drosophila_melanogaster	Brms1	FBGN0030434

Paralogs (2): SUDS3 (ENSG00000111707), BRMS1 (ENSG00000174744)

Protein

Protein identifiers

Breast cancer metastasis-suppressor 1-like protein — Q5PSV4 (reviewed: Q5PSV4)

Alternative names: BRMS1-homolog protein p40, BRMS1-like protein p40

All UniProt accessions (3): Q5PSV4, F8VRR2, H0YHD0

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the histone deacetylase (HDAC1)-dependent transcriptional repression activity. When overexpressed in lung cancer cell line that lacks p53/TP53 expression, inhibits cell growth.

Subunit / interactions. Component of the Sin3/HDAC1 corepressor complex at least composed of BRMS1, BRMS1L and ING2/ING1L. Interacts with HDAC and SIN3A.

Subcellular location. Nucleus.

Similarity. Belongs to the BRMS1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5PSV4-1	1	yes
Q5PSV4-2	2

RefSeq proteins (1): NP_115728* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013907	Sds3	Family

Pfam: PF08598

UniProt features (11 total): coiled-coil region 2, compositionally biased region 2, cross-link 2, chain 1, region of interest 1, sequence conflict 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5PSV4-F1	81.00	0.55

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 (3): 197, 240, 246

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 264 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, E2F_Q4, ELVIDGE_HYPOXIA_DN, E2F_Q4_01, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, E2F4DP1_01, TGCACTT_MIR519C_MIR519B_MIR519A, TTCCGTT_MIR191, GOBP_REGULATION_OF_PROTEIN_DEACETYLATION, GOBP_MACROMOLECULE_DEACYLATION, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, GGAMTNNNNNTCCY_UNKNOWN, chr11q13, BROWNE_HCMV_INFECTION_24HR_UP, E2F1DP1_01

GO Biological Process (6): negative regulation of transcription by RNA polymerase II (GO:0000122), negative regulation of cell migration (GO:0030336), negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512), negative regulation of stem cell population maintenance (GO:1902455), positive regulation of stem cell population maintenance (GO:1902459), regulation of gene expression (GO:0010468)

GO Molecular Function (2): histone deacetylase binding (GO:0042826), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), Sin3-type complex (GO:0070822), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
stem cell population maintenance	2
regulation of stem cell population maintenance	2
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
cell migration	1
regulation of cell migration	1
negative regulation of cell motility	1
transforming growth factor beta receptor signaling pathway	1
regulation of transforming growth factor beta receptor signaling pathway	1
negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	1
negative regulation of developmental process	1
negative regulation of multicellular organismal process	1
positive regulation of developmental process	1
positive regulation of multicellular organismal process	1
gene expression	1
regulation of macromolecule biosynthetic process	1
enzyme binding	1
binding	1
intracellular membrane-bounded organelle	1
histone deacetylase complex	1
nuclear chromosome	1
chromatin	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

788 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BRMS1L	ARID4A	P29374	986
BRMS1L	SAP30	O75446	948
BRMS1L	HDAC1	Q13547	937
BRMS1L	SIN3A	Q96ST3	905
BRMS1L	ARID4B	Q4LE39	869
BRMS1L	ING1	Q9UK53	840
BRMS1L	SAP30L	Q9HAJ7	838
BRMS1L	ING2	Q9H160	780
BRMS1L	SIN3B	O75182	743
BRMS1L	SAP18	O00422	723
BRMS1L	RBBP7	Q16576	696
BRMS1L	RBBP4	P31149	695
BRMS1L	SUDS3	Q9H7L9	676
BRMS1L	PHF12	Q96QT6	663
BRMS1L	SINHCAF	Q9NP50	655

IntAct

151 interactions, top by confidence:

A	B	Type	Score
HDAC2	KDM1A	psi-mi:“MI:0914”(association)	0.890
HDAC1	CDK2AP1	psi-mi:“MI:0914”(association)	0.840
RBBP7	CDK2AP1	psi-mi:“MI:0914”(association)	0.840
RBBP4	CDK2AP1	psi-mi:“MI:0914”(association)	0.790
HDAC1	TNRC18	psi-mi:“MI:0914”(association)	0.790
BRMS1L	ACTN2	psi-mi:“MI:0915”(physical association)	0.780
ACTN2	BRMS1L	psi-mi:“MI:0915”(physical association)	0.780
HDAC1	ZNF609	psi-mi:“MI:0914”(association)	0.730
RBBP7	HAT1	psi-mi:“MI:0914”(association)	0.730
NFIC	NFIB	psi-mi:“MI:2364”(proximity)	0.690
FOXK2	DVL2	psi-mi:“MI:0914”(association)	0.640
SINHCAF	TNRC18	psi-mi:“MI:0914”(association)	0.640
ZNF704	SAP30	psi-mi:“MI:0914”(association)	0.640
BRMS1L	DEUP1	psi-mi:“MI:0915”(physical association)	0.560
EXOC5	BRMS1L	psi-mi:“MI:0915”(physical association)	0.560
BRMS1L	MID2	psi-mi:“MI:0915”(physical association)	0.560
AMOTL2	BRMS1L	psi-mi:“MI:0915”(physical association)	0.560
DEUP1	BRMS1L	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (178): BRMS1L (Two-hybrid), BRMS1L (Two-hybrid), BRMS1L (Two-hybrid), BRMS1L (Two-hybrid), CCDC67 (Two-hybrid), BRMS1L (Affinity Capture-MS), BRMS1L (Affinity Capture-MS), BRMS1L (Affinity Capture-MS), BRMS1L (Affinity Capture-MS), BRMS1L (Affinity Capture-MS), BRMS1L (Affinity Capture-MS), BRMS1L (Affinity Capture-MS), BRMS1L (Affinity Capture-MS), BRMS1L (Affinity Capture-MS), BRMS1L (Affinity Capture-MS)

ESM2 similar proteins: A0PJP4, A2VDP1, A4FV29, A4II71, E9PSK7, F1RCP1, O00472, O60271, Q0IHE5, Q15545, Q1LZE0, Q28DG8, Q2HJG8, Q2TBQ7, Q3U1T3, Q498D5, Q4R5A5, Q4V8V1, Q58A65, Q5DTM8, Q5EA95, Q5M7T3, Q5PSV4, Q5R6Y9, Q5R7L9, Q5RHQ8, Q5VTR2, Q5ZKF4, Q5ZLL9, Q5ZLS3, Q62739, Q68CZ1, Q6AZT4, Q6DC03, Q6R1L1, Q7ZXA8, Q8BXG3, Q8CG73, Q8IZC4, Q8K0Q5

Diamond homologs: A4FV29, A4II71, Q1LZE0, Q3U1T3, Q4V8V1, Q5M7T3, Q5PSV4, Q5ZLL9, Q6AZT4, Q99N20, Q9HCU9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 115 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
Regulation of TP53 Activity through Acetylation	5	29.3×	8e-05
HDACs deacetylate histones	9	13.9×	8e-06
Negative Regulation of CDH1 Gene Transcription	8	12.3×	6e-05
Potential therapeutics for SARS	8	11.7×	6e-05
Regulation of PTEN gene transcription	5	11.4×	4e-03
NuRD complex assembly	6	10.8×	2e-03
Interaction of NuRD complexes with transcription factors	6	9.8×	3e-03
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression	5	9.8×	6e-03

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of stem cell population maintenance	10	69.0×	1e-14
positive regulation of stem cell population maintenance	10	31.0×	1e-10
negative regulation of transforming growth factor beta receptor signaling pathway	10	15.7×	1e-07
chondrocyte differentiation	5	13.6×	2e-03
somatic stem cell population maintenance	5	11.2×	4e-03
negative regulation of cell migration	11	11.1×	5e-07
response to wounding	5	10.0×	6e-03
animal organ morphogenesis	5	8.6×	1e-02

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	0
Uncertain significance	28
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
147567	GRCh38/hg38 14q13.2-13.3(chr14:35514078-36814016)x1	Pathogenic
148775	GRCh38/hg38 14q13.2-21.2(chr14:35068276-43994777)x1	Pathogenic
1527808	GRCh37/hg19 14q13.2-21.1(chr14:35850213-40138562)	Pathogenic
564135	GRCh37/hg19 14q13.2-21.2(chr14:35934503-47120961)x1	Pathogenic
57774	GRCh38/hg38 14q13.2(chr14:35696014-36030164)x1	Pathogenic

SpliceAI

2014 predictions. Top by Δscore:

Variant	Effect	Δscore
14:35826656:CAGGT:C	donor_loss	1.0000
14:35831402:A:AG	acceptor_gain	1.0000
14:35831403:T:G	acceptor_gain	1.0000
14:35831405:A:AG	acceptor_gain	1.0000
14:35831406:ACAG:A	acceptor_loss	1.0000
14:35831408:A:AG	acceptor_gain	1.0000
14:35831408:A:AT	acceptor_loss	1.0000
14:35831409:G:GT	acceptor_gain	1.0000
14:35831409:GA:G	acceptor_gain	1.0000
14:35831409:GAA:G	acceptor_gain	1.0000
14:35831409:GAAA:G	acceptor_gain	1.0000
14:35831409:GAAAT:G	acceptor_gain	1.0000
14:35831496:GATCA:G	donor_gain	1.0000
14:35831497:A:G	donor_gain	1.0000
14:35831497:ATCA:A	donor_gain	1.0000
14:35831498:TCA:T	donor_gain	1.0000
14:35831499:CA:C	donor_gain	1.0000
14:35831500:AGT:A	donor_loss	1.0000
14:35831501:G:GG	donor_gain	1.0000
14:35831502:T:G	donor_loss	1.0000
14:35832974:TAAG:T	acceptor_gain	1.0000
14:35832975:A:AG	acceptor_gain	1.0000
14:35832975:AAGA:A	acceptor_gain	1.0000
14:35832976:A:AG	acceptor_gain	1.0000
14:35832977:G:GG	acceptor_gain	1.0000
14:35832977:GA:G	acceptor_gain	1.0000
14:35833075:GAAAA:G	donor_gain	1.0000
14:35833076:A:T	donor_gain	1.0000
14:35862587:CAGAG:C	acceptor_gain	1.0000
14:35862588:A:AG	acceptor_gain	1.0000

AlphaMissense

2150 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:35831438:A:C	R57S	1.000
14:35831438:A:T	R57S	1.000
14:35831441:A:C	R58S	1.000
14:35831441:A:T	R58S	1.000
14:35831461:T:C	M65T	1.000
14:35831461:T:G	M65R	1.000
14:35831470:T:A	L68H	1.000
14:35831470:T:C	L68P	1.000
14:35831481:T:A	F72I	1.000
14:35831481:T:C	F72L	1.000
14:35831482:T:C	F72S	1.000
14:35831482:T:G	F72C	1.000
14:35831483:T:A	F72L	1.000
14:35831483:T:G	F72L	1.000
14:35831491:T:C	L75P	1.000
14:35831494:A:T	K76I	1.000
14:35831495:A:C	K76N	1.000
14:35831495:A:T	K76N	1.000
14:35832980:T:C	L79P	1.000
14:35832992:G:C	R83P	1.000
14:35833016:T:C	L91P	1.000
14:35833025:T:A	V94D	1.000
14:35833048:T:C	Y102H	1.000
14:35833048:T:G	Y102D	1.000
14:35833061:T:C	L106P	1.000
14:35833091:G:C	R116P	1.000
14:35833102:G:C	A120P	1.000
14:35834859:T:C	L126P	1.000
14:35834903:G:C	A141P	1.000
14:35834904:C:A	A141D	1.000

dbSNP variants (sampled 300 via entrez): RS1000037687 (14:35842601 C>T), RS1000041286 (14:35849237 A>G), RS1000142094 (14:35839537 C>T), RS1000185414 (14:35834438 G>C), RS1000237064 (14:35846334 T>C), RS1000253781 (14:35827932 C>T), RS1000430180 (14:35842978 T>C), RS1000488467 (14:35864856 A>G), RS1000551956 (14:35838186 C>G), RS1000703867 (14:35829607 G>A), RS1000772793 (14:35828209 G>A), RS1000773086 (14:35866650 A>G), RS1000778615 (14:35832166 G>A), RS1000902267 (14:35826034 G>A), RS1000937313 (14:35867583 T>C)

Disease associations

OMIM: gene MIM:618514 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression	2
Valproic Acid	affects expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	2
FR900359	decreases phosphorylation	1
TAK-243	decreases sumoylation	1
dicrotophos	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
azoxystrobin	decreases expression	1
deguelin	decreases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
jinfukang	affects cotreatment, increases expression, decreases expression	1
Vorinostat	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cadmium	increases abundance, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Demecolcine	increases expression	1
Dimethyl Sulfoxide	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Rotenone	decreases expression	1
Urethane	increases expression	1
Aflatoxin B1	increases expression	1
Aflatoxin M1	decreases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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