BMERB1

Summary

BMERB1 (bMERB domain containing 1, HGNC:19213) is a protein-coding gene on chromosome 16p13.11, encoding bMERB domain-containing protein 1 (Q96MC5).

Predicted to be involved in negative regulation of microtubule depolymerization. Predicted to act upstream of or within negative regulation of cell motility involved in cerebral cortex radial glia guided migration. Predicted to be active in microtubule cytoskeleton.

Source: NCBI Gene 89927 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 23 total — 5 pathogenic, 4 likely-pathogenic
• MANE Select transcript: NM_033201

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19213
Approved symbol	BMERB1
Name	bMERB domain containing 1
Location	16p13.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32618
Ensembl gene	ENSG00000166780
Ensembl biotype	protein_coding
Entrez	89927

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000300006, ENST00000452191, ENST00000561692, ENST00000561813, ENST00000563380, ENST00000564389, ENST00000565857, ENST00000565913, ENST00000566490, ENST00000567550, ENST00000570249, ENST00000869050, ENST00000962100, ENST00000962101, ENST00000962102

RefSeq mRNA: 3 — MANE Select: NM_033201 NM_001142469, NM_001414674, NM_033201

CCDS: CCDS10561, CCDS45422

Canonical transcript exons

ENST00000300006 — 6 exons

Exon	Start	End
ENSE00001131222	15586717	15588259
ENSE00002591059	15434588	15434759
ENSE00003475728	15581217	15581331
ENSE00003526647	15567983	15568056
ENSE00003535637	15583156	15583238
ENSE00003601467	15515305	15515428

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 98.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.0874 / max 674.6199, expressed in 1509 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152894	9.8525	1439
152897	6.5150	1113
152896	2.1635	792
152895	1.5518	634
152900	0.0045	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
superior frontal gyrus	UBERON:0002661	98.97	gold quality
primary visual cortex	UBERON:0002436	98.94	gold quality
prefrontal cortex	UBERON:0000451	98.84	gold quality
frontal cortex	UBERON:0001870	98.69	gold quality
cortical plate	UBERON:0005343	98.64	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.55	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.49	gold quality
cerebral cortex	UBERON:0000956	98.43	gold quality
right frontal lobe	UBERON:0002810	98.41	gold quality
anterior cingulate cortex	UBERON:0009835	98.13	gold quality
Ammon’s horn	UBERON:0001954	97.93	gold quality
temporal lobe	UBERON:0001871	97.91	gold quality
amygdala	UBERON:0001876	97.89	gold quality
hypothalamus	UBERON:0001898	97.73	gold quality
cerebellum	UBERON:0002037	97.52	gold quality
cerebellar cortex	UBERON:0002129	97.50	gold quality
cerebellar hemisphere	UBERON:0002245	97.49	gold quality
brain	UBERON:0000955	97.34	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.28	gold quality
nucleus accumbens	UBERON:0001882	97.07	gold quality
ganglionic eminence	UBERON:0004023	96.93	gold quality
putamen	UBERON:0001874	96.42	gold quality
caudate nucleus	UBERON:0001873	96.29	gold quality
substantia nigra	UBERON:0002038	95.99	gold quality
popliteal artery	UBERON:0002250	95.73	gold quality
tibial artery	UBERON:0007610	95.72	gold quality
islet of Langerhans	UBERON:0000006	95.54	gold quality
right coronary artery	UBERON:0001625	95.41	gold quality
mucosa of stomach	UBERON:0001199	95.36	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.21	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	12.38
E-ANND-3	yes	11.71
E-HCAD-31	no	5.33
E-HCAD-5	no	2.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting BMERB1, 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-8485	100.00	77.57	4731
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-3659	99.70	67.97	694
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-548U	99.65	67.78	1463
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-4489	99.50	65.56	785
HSA-MIR-4498	99.47	67.42	2360

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	bmerb1	ENSDARG00000086706
mus_musculus	Bmerb1	ENSMUSG00000044117
rattus_norvegicus	Bmerb1	ENSRNOG00000003198

Protein

Protein identifiers

bMERB domain-containing protein 1 — Q96MC5 (reviewed: Q96MC5)

All UniProt accessions (7): Q96MC5, H3BP34, H3BR56, H3BRF6, H3BTT5, H3BU79, H3BUY6

Isoforms (2)

UniProt ID	Names	Canonical?
Q96MC5-1	1	yes
Q96MC5-2	2

RefSeq proteins (3): NP_001135941, NP_001401603, NP_149978* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022735	bMERB_dom	Domain
IPR040127	BMERB	Family

Pfam: PF12130

UniProt features (4 total): chain 1, domain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96MC5-F1	74.19	0.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 169 (showing top): GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, TGCGCANK_UNKNOWN, GOBP_LAYER_FORMATION_IN_CEREBRAL_CORTEX, GOBP_NEUROGENESIS, GOBP_FOREBRAIN_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_FOREBRAIN_CELL_MIGRATION, MODULE_66, MARTINEZ_RB1_TARGETS_UP, CATTTCA_MIR203, ONKEN_UVEAL_MELANOMA_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_MICROTUBULE_DEPOLYMERIZATION, GOBP_TELENCEPHALON_GLIAL_CELL_MIGRATION, GOBP_CEREBRAL_CORTEX_DEVELOPMENT

GO Biological Process (4): microtubule depolymerization (GO:0007019), negative regulation of microtubule depolymerization (GO:0007026), cell motility involved in cerebral cortex radial glia guided migration (GO:0021814), negative regulation of cell motility involved in cerebral cortex radial glia guided migration (GO:0021822)

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

GO Cellular Component (1): microtubule cytoskeleton (GO:0015630)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
microtubule polymerization or depolymerization	1
protein depolymerization	1
supramolecular fiber organization	1
microtubule depolymerization	1
negative regulation of microtubule polymerization or depolymerization	1
regulation of microtubule depolymerization	1
negative regulation of protein depolymerization	1
negative regulation of supramolecular fiber organization	1
cerebral cortex radial glia-guided migration	1
cell motility	1
cell motility involved in cerebral cortex radial glia guided migration	1
layer formation in cerebral cortex	1
negative regulation of glial cell migration	1
binding	1
cytoskeleton	1

Protein interactions and networks

STRING

272 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BMERB1	SDHB	P21912	791
BMERB1	CEP20	Q96NB1	716
BMERB1	MARF1	Q9Y4F3	647
BMERB1	MPV17L	Q2QL34	507
BMERB1	H3BMD7	H3BMD7	480
BMERB1	NDE1	Q9NXR1	452
BMERB1	PRKAR1B	P31321	448
BMERB1	MAP7D2	Q96T17	416
BMERB1	RBFOX1	Q9NWB1	400
BMERB1	RPL19	P14118	391
BMERB1	ABCC6	P78420	371
BMERB1	PDXDC1	Q6P996	366
BMERB1	PIAS2	O75928	359
BMERB1	A0A0A6YYJ8	A0A0A6YYJ8	358
BMERB1	NOMO3	P69849	357
BMERB1	KLC1	Q07866	357

IntAct

17 interactions, top by confidence:

A	B	Type	Score
SGF29	NDC80	psi-mi:“MI:0914”(association)	0.840
RAPGEF4	BMERB1	psi-mi:“MI:0915”(physical association)	0.670
BMERB1	RAPGEF4	psi-mi:“MI:0915”(physical association)	0.670
TCF12	BMERB1	psi-mi:“MI:0915”(physical association)	0.560
BMERB1	DCTN6	psi-mi:“MI:0914”(association)	0.530
RAPGEF4	BMERB1	psi-mi:“MI:0915”(physical association)	0.370
NP	BMERB1	psi-mi:“MI:0915”(physical association)	0.370
	SHTN1	psi-mi:“MI:0914”(association)	0.350
BMERB1	SPAG9	psi-mi:“MI:0914”(association)	0.350
BMERB1	ENO2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (43): C16orf45 (Two-hybrid), C16orf45 (Two-hybrid), BFSP1 (Affinity Capture-MS), CCDC101 (Affinity Capture-MS), ZYG11A (Affinity Capture-MS), SPAG9 (Affinity Capture-MS), UBR3 (Affinity Capture-MS), POLE (Affinity Capture-MS), ACTR10 (Affinity Capture-MS), POLE2 (Affinity Capture-MS), ACTR1B (Affinity Capture-MS), ATE1 (Affinity Capture-MS), DCTN4 (Affinity Capture-MS), DCTN6 (Affinity Capture-MS), WDFY1 (Affinity Capture-MS)

ESM2 similar proteins: A0A088MLT8, A2AQ19, A4FV29, A4IFK9, B3KU38, O14795, O70166, O93388, O95983, P21818, P31395, P50751, P54227, P55821, P63042, P63043, Q09001, Q09002, Q09004, Q09006, Q2KJ58, Q32L68, Q4KUS2, Q4R4N5, Q5F3L9, Q5FVJ5, Q5PSV4, Q5R4C5, Q5R562, Q5R8C6, Q5RAD5, Q62768, Q6GQB5, Q8IVM0, Q8IW50, Q8TBN0, Q8VDV3, Q90987, Q92541, Q93045

Diamond homologs: D3ZEN0, Q3TN34, Q5FVJ5, Q5R562, Q8IY33, Q8R1Y2, Q96MC5, D3ZQL6, E1BBG2, Q8BGT6, Q8N3F8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	4
Uncertain significance	4
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (9)

Variant ID	HGVS	Classification
2685561	GRCh37/hg19 16p13.11(chr16:15450290-16458408)x1	Pathogenic
2685562	GRCh37/hg19 16p13.11(chr16:15481748-16391045)x1	Pathogenic
625569	GRCh37/hg19 16p13.11(chr16:15125627-16286750)	Pathogenic
625574	GRCh37/hg19 16p13.11(chr16:15521713-16292235)	Pathogenic
815803	GRCh37/hg19 16p13.11-12.3(chr16:15416364-18231275)x1	Pathogenic
1808886	GRCh37/hg19 16p13.11(chr16:15509407-15858075)x3	Likely pathogenic
815799	GRCh37/hg19 16p13.11-12.3(chr16:14900168-16869135)x3	Likely pathogenic
815800	GRCh37/hg19 16p13.11(chr16:14900182-16529801)x3	Likely pathogenic
980077	GRCh37/hg19 16p13.11(chr16:14929038-16309046)x3	Likely pathogenic

SpliceAI

4731 predictions. Top by Δscore:

Variant	Effect	Δscore
16:15434755:GAGAA:G	donor_gain	1.0000
16:15434757:GAA:G	donor_gain	1.0000
16:15434757:GAAGT:G	donor_loss	1.0000
16:15434758:AA:A	donor_gain	1.0000
16:15434759:AG:A	donor_loss	1.0000
16:15434760:G:GG	donor_gain	1.0000
16:15434760:GT:G	donor_loss	1.0000
16:15515300:CACA:C	acceptor_loss	1.0000
16:15515301:A:AG	acceptor_gain	1.0000
16:15515301:ACAG:A	acceptor_loss	1.0000
16:15515302:C:G	acceptor_gain	1.0000
16:15515302:CA:C	acceptor_loss	1.0000
16:15515303:A:AG	acceptor_gain	1.0000
16:15515303:AGA:A	acceptor_loss	1.0000
16:15515304:G:GA	acceptor_gain	1.0000
16:15515304:GAT:G	acceptor_gain	1.0000
16:15515304:GATC:G	acceptor_gain	1.0000
16:15515304:GATCA:G	acceptor_gain	1.0000
16:15515391:G:GT	donor_gain	1.0000
16:15515391:G:T	donor_gain	1.0000
16:15515429:G:GG	donor_gain	1.0000
16:15567980:CA:C	acceptor_loss	1.0000
16:15567981:A:AG	acceptor_gain	1.0000
16:15567981:AG:A	acceptor_gain	1.0000
16:15567981:AGGAT:A	acceptor_gain	1.0000
16:15567982:G:GG	acceptor_gain	1.0000
16:15567982:GG:G	acceptor_gain	1.0000
16:15567982:GGAT:G	acceptor_gain	1.0000
16:15567982:GGATG:G	acceptor_gain	1.0000
16:15568053:CCAGG:C	donor_loss	1.0000

AlphaMissense

1352 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:15515419:T:C	L74P	0.999
16:15515407:G:C	R70P	0.998
16:15515412:T:C	S72P	0.998
16:15568033:T:C	L94P	0.997
16:15581293:A:C	R127S	0.997
16:15581293:A:T	R127S	0.997
16:15583156:G:C	R140S	0.997
16:15583156:G:T	R140S	0.997
16:15568000:T:C	L83P	0.996
16:15581259:T:C	L116P	0.996
16:15581325:G:C	R138P	0.996
16:15581331:G:C	R140T	0.996
16:15515389:G:C	R64P	0.995
16:15515403:C:A	R69S	0.995
16:15515404:G:C	R69P	0.995
16:15515424:T:C	F76L	0.995
16:15515426:C:A	F76L	0.995
16:15515426:C:G	F76L	0.995
16:15581301:T:C	L130P	0.995
16:15581312:G:C	A134P	0.995
16:15515386:T:C	L63P	0.994
16:15567991:A:T	D80V	0.994
16:15581280:T:C	L123P	0.994
16:15581292:G:C	R127T	0.994
16:15581292:G:T	R127I	0.994
16:15581331:G:T	R140M	0.994
16:15583169:G:C	D145H	0.994
16:15515419:T:A	L74H	0.992
16:15515425:T:C	F76S	0.992
16:15567990:G:C	D80H	0.992

dbSNP variants (sampled 300 via entrez): RS1000024287 (16:15587867 G>A), RS1000027925 (16:15528908 G>A), RS1000029509 (16:15493410 A>G), RS1000036730 (16:15504750 G>C), RS1000036995 (16:15535462 A>G), RS1000046282 (16:15487238 C>G,T), RS1000063800 (16:15499655 C>G), RS1000077138 (16:15448417 C>T), RS1000086540 (16:15503811 G>A), RS1000112544 (16:15512120 T>C), RS1000117836 (16:15522792 T>C), RS1000141843 (16:15541012 A>G), RS1000172529 (16:15504509 A>T), RS1000189440 (16:15555589 G>A), RS1000199037 (16:15585761 G>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST002444_7	Plasma omega-6 polyunsaturated fatty acid levels (dihomo-gamma-linolenic acid)	2.000000e-67
GCST002444_8	Plasma omega-6 polyunsaturated fatty acid levels (dihomo-gamma-linolenic acid)	5.000000e-25
GCST002446_5	Plasma omega-6 polyunsaturated fatty acid levels (linoleic acid)	1.000000e-15
GCST002446_6	Plasma omega-6 polyunsaturated fatty acid levels (linoleic acid)	3.000000e-06
GCST002446_8	Plasma omega-6 polyunsaturated fatty acid levels (linoleic acid)	4.000000e-14
GCST002450_10	Plasma omega-6 polyunsaturated fatty acid levels (gamma-linolenic acid)	2.000000e-12
GCST90001389_4	Creutzfeldt-Jakob disease (sporadic)	6.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005680	omega-6 polyunsaturated fatty acid measurement
EFO:1000656	sporadic Creutzfeld Jacob disease

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Estradiol	affects cotreatment, decreases expression, increases expression	4
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	3
Aflatoxin B1	decreases expression, increases methylation	3
Benzo(a)pyrene	affects methylation, decreases expression	2
Valproic Acid	affects expression, increases expression	2
methyleugenol	decreases expression	1
bisphenol A	affects cotreatment, increases methylation	1
terbufos	increases methylation	1
tris(2-butoxyethyl) phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
2,2’,4,4’,5-brominated diphenyl ether	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Calcitriol	increases expression	1
Coumestrol	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	decreases expression	1
Fonofos	increases methylation	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Parathion	increases methylation	1

Clinical trials (associated diseases)

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