CDC50B

Summary

CDC50B (cell division cycle 50 P4-ATPase accessory subunit B, HGNC:27254) is a protein-coding gene on chromosome 14q23.1, encoding Cell cycle control protein 50B (Q3MIR4). Accessory component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids.

Enables aminophospholipid flippase activity. Involved in aminophospholipid transport and positive regulation of protein exit from endoplasmic reticulum. Located in plasma membrane. Part of phospholipid-translocating ATPase complex.

Source: NCBI Gene 161291 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001017970

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27254
Approved symbol	CDC50B
Name	cell division cycle 50 P4-ATPase accessory subunit B
Location	14q23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000182107
Ensembl biotype	protein_coding
OMIM	611029
Entrez	161291

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000554497, ENST00000555868, ENST00000557163

RefSeq mRNA: 1 — MANE Select: NM_001017970 NM_001017970

CCDS: CCDS32093

Canonical transcript exons

ENST00000555868 — 1 exons

Exon	Start	End
ENSE00002442160	61277370	61281338

Expression profiles

Bgee: expression breadth ubiquitous, 232 present calls, max score 97.56.

FANTOM5 (CAGE): breadth broad, TPM avg 8.7974 / max 220.7504, expressed in 637 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter ID	TPM avg	Samples expressed
143534	2.7317	386
143531	2.5337	341
143535	0.9423	307
143537	0.6066	280
143538	0.4093	228
143532	0.3954	211
143542	0.3464	161
143536	0.2706	186
143530	0.1957	120
143533	0.1248	72

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of sigmoid colon	UBERON:0004993	97.56	gold quality
colonic mucosa	UBERON:0000317	97.44	gold quality
bronchial epithelial cell	CL:0002328	97.05	gold quality
jejunal mucosa	UBERON:0000399	96.17	gold quality
corpus epididymis	UBERON:0004359	95.92	gold quality
epithelium of bronchus	UBERON:0002031	95.57	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.40	gold quality
ileal mucosa	UBERON:0000331	95.24	gold quality
bronchus	UBERON:0002185	95.22	gold quality
duodenum	UBERON:0002114	94.76	gold quality
palpebral conjunctiva	UBERON:0001812	94.56	gold quality
type B pancreatic cell	CL:0000169	93.71	gold quality
caput epididymis	UBERON:0004358	93.56	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.41	gold quality
nasal cavity epithelium	UBERON:0005384	93.36	gold quality
nasal cavity mucosa	UBERON:0001826	93.32	gold quality
islet of Langerhans	UBERON:0000006	92.72	gold quality
parotid gland	UBERON:0001831	91.50	gold quality
seminal vesicle	UBERON:0000998	91.38	gold quality
thyroid gland	UBERON:0002046	90.92	gold quality
left lobe of thyroid gland	UBERON:0001120	90.81	gold quality
esophagus squamous epithelium	UBERON:0006920	90.80	gold quality
rectum	UBERON:0001052	90.73	gold quality
gall bladder	UBERON:0002110	90.17	gold quality
epithelium of esophagus	UBERON:0001976	89.72	gold quality
right lobe of thyroid gland	UBERON:0001119	89.42	gold quality
epithelial cell of pancreas	CL:0000083	89.26	gold quality
mucosa of transverse colon	UBERON:0004991	89.07	gold quality
pancreas	UBERON:0001264	89.06	gold quality
oral cavity	UBERON:0000167	88.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

79 targeting CDC50B, 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-7110-3P	100.00	73.18	2486
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-4658	99.77	64.94	514

Literature-anchored findings (GeneRIF, showing 1)

• Downregulation of TMEM30B is associated with recurrence in meningiomas. (PMID:20685720)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem30b	ENSDARG00000054122
mus_musculus	Tmem30b	ENSMUSG00000034435
rattus_norvegicus	Tmem30b	ENSRNOG00000008046
drosophila_melanogaster	Cdc50	FBGN0030752
caenorhabditis_elegans		WBGENE00008969
caenorhabditis_elegans		WBGENE00012224
caenorhabditis_elegans		WBGENE00019946

Paralogs (1): TMEM30A (ENSG00000112697)

Protein

Protein identifiers

Cell cycle control protein 50B — Q3MIR4 (reviewed: Q3MIR4)

Alternative names: P4-ATPase flippase complex beta subunit TMEM30B, Transmembrane protein 30B

All UniProt accessions (1): Q3MIR4

UniProt curated annotations — full annotation on UniProt →

Function. Accessory component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids. Phospholipid translocation also seems to be implicated in vesicle formation and in uptake of lipid signaling molecules. The beta subunit may assist in binding of the phospholipid substrate. Can mediate the export of alpha subunits ATP8A1, ATP8B1, ATP8B2 and ATP8B4 from the ER to the plasma membrane.

Subunit / interactions. Component of a P4-ATPase flippase complex which consists of a catalytic alpha subunit and an accessory beta subunit. Interacts with alpha subunits ATP8A1, ATP8B1, ATP8B2 and ATP8B4.

Subcellular location. Cell membrane. Endoplasmic reticulum membrane.

Similarity. Belongs to the CDC50/LEM3 family.

RefSeq proteins (1): NP_001017970* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005045	CDC50/LEM3_fam	Family

Pfam: PF03381

UniProt features (33 total): helix 11, strand 10, topological domain 3, turn 3, glycosylation site 3, transmembrane region 2, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7VGH	ELECTRON MICROSCOPY	3.39

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3MIR4-F1	92.44	0.82

Functional residue map

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

Glycosylation sites (3): 75, 213, 286

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_REGULATION_OF_MEMBRANE_LIPID_DISTRIBUTION, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_TRANSPORT, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, DAWSON_METHYLATED_IN_LYMPHOMA_TCL1, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, GOBP_REGULATION_OF_CELLULAR_LOCALIZATION, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_6, GOBP_REGULATION_OF_INTRACELLULAR_PROTEIN_TRANSPORT, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, AIGNER_ZEB1_TARGETS

GO Biological Process (5): aminophospholipid transport (GO:0015917), phospholipid translocation (GO:0045332), positive regulation of protein exit from endoplasmic reticulum (GO:0070863), lipid transport (GO:0006869), aminophospholipid translocation (GO:0140331)

GO Molecular Function (2): aminophospholipid flippase activity (GO:0015247), protein binding (GO:0005515)

GO Cellular Component (6): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), phospholipid-translocating ATPase complex (GO:1990531), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
phospholipid transport	2
cytoplasm	2
endomembrane system	2
intracellular membrane-bounded organelle	2
nitrogen compound transport	1
lipid translocation	1
protein exit from endoplasmic reticulum	1
regulation of protein exit from endoplasmic reticulum	1
positive regulation of intracellular protein transport	1
transport	1
lipid localization	1
aminophospholipid transport	1
phospholipid translocation	1
flippase activity	1
aminophospholipid translocation	1
binding	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
membrane	1
cell periphery	1
transporter complex	1
cellular anatomical structure	1

Protein interactions and networks

STRING

776 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDC50B	ATP8B1	O43520	768
CDC50B	ATP8B2	P98198	766
CDC50B	ATP8B4	Q8TF62	746
CDC50B	ATP9B	O43861	643
CDC50B	ATP9A	O75110	642
CDC50B	ATP8A2	Q9NTI2	631
CDC50B	ATP8A1	Q9Y2Q0	605
CDC50B	ATP11C	Q8NB49	604
CDC50B	KAZALD1	Q96I82	581
CDC50B	ATP10D	Q9P241	551
CDC50B	ATP8B3	O60423	550
CDC50B	ATP10B	O94823	520
CDC50B	TMEM25	Q86YD3	493
CDC50B	ATP11B	Q9Y2G3	490
CDC50B	ATP11A	P98196	490

IntAct

30 interactions, top by confidence:

A	B	Type	Score
TMEM30B	ATP8B1	psi-mi:“MI:0915”(physical association)	0.740
ATP8B1	TMEM30B	psi-mi:“MI:0915”(physical association)	0.740
ATP8B1	TMEM30B	psi-mi:“MI:0403”(colocalization)	0.740
TMEM30B	ATP8B1	psi-mi:“MI:0403”(colocalization)	0.740
TMEM30B	ATP8B2	psi-mi:“MI:0915”(physical association)	0.620
TMEM30B	ATP8B2	psi-mi:“MI:0403”(colocalization)	0.620
ATP8B2	TMEM30B	psi-mi:“MI:0915”(physical association)	0.620
ATP8B4	TMEM30B	psi-mi:“MI:0915”(physical association)	0.570
ATP8B4	TMEM30B	psi-mi:“MI:0403”(colocalization)	0.570
TMEM30B	ATP8B4	psi-mi:“MI:0403”(colocalization)	0.570
SFTPC	TMEM30B	psi-mi:“MI:0915”(physical association)	0.560
SCD	TMEM30B	psi-mi:“MI:0915”(physical association)	0.560
PMP22	TMEM30B	psi-mi:“MI:0915”(physical association)	0.560
GPR42	TMEM30B	psi-mi:“MI:0915”(physical association)	0.560
TMEM30B	KLRG2	psi-mi:“MI:0914”(association)	0.530
ATP8A1	TMEM30B	psi-mi:“MI:0915”(physical association)	0.460
ATP8A1	TMEM30B	psi-mi:“MI:0403”(colocalization)	0.460
	SHTN1	psi-mi:“MI:0914”(association)	0.350
	TMEM223	psi-mi:“MI:0914”(association)	0.350
SFTPC	TMEM30B	psi-mi:“MI:0915”(physical association)	0.000
SCD	TMEM30B	psi-mi:“MI:0915”(physical association)	0.000
PMP22	TMEM30B	psi-mi:“MI:0915”(physical association)	0.000
TMEM30B	GPR42	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (149): PCDH17 (Affinity Capture-MS), PRTG (Affinity Capture-MS), SGCE (Affinity Capture-MS), IGDCC4 (Affinity Capture-MS), PCDHGA11 (Affinity Capture-MS), TYRO3 (Affinity Capture-MS), FGFR4 (Affinity Capture-MS), TMEM230 (Affinity Capture-MS), FGFR2 (Affinity Capture-MS), PODXL2 (Affinity Capture-MS), PCDHGC4 (Affinity Capture-MS), PVRL2 (Affinity Capture-MS), FGFR3 (Affinity Capture-MS), MAN1A1 (Affinity Capture-MS), SDK2 (Affinity Capture-MS)

ESM2 similar proteins: A8X4W9, A8XKF2, F8W463, G0SDN0, H2L0H3, O15118, O35604, P05029, P21188, P25169, P25656, P30715, P30716, P33879, P42838, P43002, P49654, P51577, P51578, P51579, P53740, P54709, P56373, P56941, P97370, Q17QL5, Q1MTQ5, Q202B1, Q24046, Q2T9P5, Q3MIR4, Q3T0C6, Q3UR32, Q5E9U1, Q5R6C0, Q60489, Q63377, Q6AY41, Q8BHG3, Q8VEK0

Diamond homologs: A0ZT23, G0SDN0, H2L0H3, P25656, P53740, Q17QL5, Q1MTQ5, Q2T9P5, Q3MIR4, Q5F362, Q5R6C0, Q67YS6, Q6AY41, Q8BHG3, Q8L8W0, Q8VEK0, Q95JK4, Q96WW4, Q9D4D7, Q9LTW0, Q9NV96, Q9SA35, Q9SLK2, P42838, A0ZSE6, S7WII9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

63 predictions. Top by Δscore:

Variant	Effect	Δscore
14:61277526:AGCCT:A	acceptor_gain	0.8900
14:61277527:GCCTG:G	acceptor_gain	0.8900
14:61280923:G:C	donor_gain	0.6800
14:61281448:CCTCA:C	donor_loss	0.5200
14:61281449:CTCAC:C	donor_loss	0.5200
14:61281451:CA:C	donor_loss	0.5200
14:61281452:A:T	donor_loss	0.5200
14:61281454:C:G	donor_loss	0.5100
14:61281447:ACCT:A	donor_loss	0.4800
14:61277528:CCT:C	acceptor_gain	0.4400
14:61280842:C:A	acceptor_gain	0.4400
14:61280076:C:A	donor_gain	0.4200
14:61280929:G:T	donor_gain	0.4200
14:61281444:T:TC	donor_gain	0.4100
14:61280921:CAG:C	donor_gain	0.3900
14:61281455:T:A	donor_loss	0.3900
14:61280928:C:CT	donor_gain	0.3800
14:61281445:TTACC:T	donor_loss	0.3800
14:61281446:TACCT:T	donor_loss	0.3800
14:61280854:G:GT	acceptor_gain	0.3700
14:61281071:C:CT	acceptor_gain	0.3600
14:61281089:T:G	acceptor_gain	0.3600
14:61281071:C:A	acceptor_gain	0.3300
14:61277526:AGC:A	acceptor_gain	0.3200
14:61281022:C:CT	acceptor_gain	0.3100
14:61280038:A:C	donor_gain	0.3000
14:61280847:G:GT	acceptor_gain	0.3000
14:61277525:AAGCC:A	acceptor_gain	0.2900
14:61281476:T:TA	donor_loss	0.2900
14:61280040:C:T	donor_gain	0.2800

AlphaMissense

2270 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:61280248:C:A	K300N	0.998
14:61280248:C:G	K300N	0.998
14:61280362:G:C	F262L	0.998
14:61280362:G:T	F262L	0.998
14:61280364:A:G	F262L	0.998
14:61280389:C:A	W253C	0.998
14:61280389:C:G	W253C	0.998
14:61280391:A:G	W253R	0.998
14:61280391:A:T	W253R	0.998
14:61280530:G:C	F206L	0.998
14:61280530:G:T	F206L	0.998
14:61280532:A:G	F206L	0.998
14:61280633:T:A	D172V	0.998
14:61280634:C:G	D172H	0.998
14:61280660:C:A	G163V	0.998
14:61280663:C:T	C162Y	0.998
14:61280791:C:A	Q119H	0.998
14:61280791:C:G	Q119H	0.998
14:61280660:C:T	G163D	0.997
14:61280662:G:C	C162W	0.997
14:61280663:C:A	C162F	0.997
14:61280666:G:T	P161H	0.997
14:61280788:G:C	N120K	0.997
14:61280788:G:T	N120K	0.997
14:61280357:T:A	K264I	0.996
14:61280461:C:A	W229C	0.996
14:61280461:C:G	W229C	0.996
14:61280554:C:A	W198C	0.996
14:61280554:C:G	W198C	0.996
14:61280633:T:G	D172A	0.996

dbSNP variants (sampled 300 via entrez): RS1000015382 (14:61279928 GCCCC>G,GCC,GCCC,GCCCCC), RS1000209640 (14:61280367 T>C,G), RS1002319814 (14:61281511 T>A,C), RS1003597575 (14:61277187 G>A), RS1004699732 (14:61282829 C>T), RS1004721741 (14:61277604 T>C), RS1006317747 (14:61277295 T>C), RS1006846172 (14:61279461 A>G), RS1007224341 (14:61278926 AT>A,ATT), RS1007677167 (14:61280323 C>A,G), RS1008420825 (14:61281534 G>C), RS1010097892 (14:61280631 A>T), RS1010178857 (14:61281941 T>C), RS1010523340 (14:61282046 G>A), RS1011026330 (14:61276905 C>T)

Disease associations

OMIM: gene MIM:611029 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001762_638	Obesity-related traits	3.000000e-06
GCST002928_8	Nickel levels	8.000000e-06
GCST004068_60	Venous thromboembolism adjusted for sickle cell variant rs77121243-T	5.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects cotreatment	5
trichostatin A	increases expression, affects cotreatment	3
bisphenol A	decreases expression, affects cotreatment, increases expression	2
mercuric bromide	increases expression, affects cotreatment	2
entinostat	increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Air Pollutants	increases abundance, increases expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
Particulate Matter	increases abundance, increases expression	2
GSK-J4	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
Acetaminophen	decreases expression	1
Calcitriol	increases expression	1
Carbamazepine	affects expression	1
Copper	decreases expression, affects binding	1
Dexamethasone	affects cotreatment, increases expression	1
Drugs, Chinese Herbal	decreases expression	1
Estradiol	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Tretinoin	increases expression	1

Clinical trials (associated diseases)

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