TMEM54

Summary

TMEM54 (transmembrane protein 54, HGNC:24143) is a protein-coding gene on chromosome 1p35.1, encoding Transmembrane protein 54 (Q969K7).

Predicted to be located in membrane.

Source: NCBI Gene 113452 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 58 total — 1 likely-pathogenic
• MANE Select transcript: NM_033504

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24143
Approved symbol	TMEM54
Name	transmembrane protein 54
Location	1p35.1
Locus type	gene with protein product
Status	Approved
Aliases	CAC-1, BCLP
Ensembl gene	ENSG00000121900
Ensembl biotype	protein_coding
Entrez	113452

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 13 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000329151, ENST00000373463, ENST00000463914, ENST00000474144, ENST00000475208, ENST00000482771, ENST00000854966, ENST00000854967, ENST00000854968, ENST00000935360, ENST00000935361, ENST00000947217, ENST00000947218, ENST00000947219, ENST00000947220, ENST00000947221, ENST00000947222

RefSeq mRNA: 5 — MANE Select: NM_033504 NM_001329722, NM_001329723, NM_001329724, NM_001329725, NM_033504

CCDS: CCDS371, CCDS85954

Canonical transcript exons

ENST00000373463 — 6 exons

Exon	Start	End
ENSE00001310507	32894595	32894879
ENSE00001409583	32901223	32901389
ENSE00003543541	32898126	32898319
ENSE00003581458	32895555	32895743
ENSE00003604850	32895305	32895439
ENSE00003685424	32895910	32895969

Expression profiles

Bgee: expression breadth ubiquitous, 209 present calls, max score 99.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.2354 / max 166.6044, expressed in 1475 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11566	10.2354	1475

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	99.67	gold quality
ileal mucosa	UBERON:0000331	99.64	gold quality
lower esophagus mucosa	UBERON:0035834	98.54	gold quality
transverse colon	UBERON:0001157	97.65	gold quality
rectum	UBERON:0001052	97.57	gold quality
colonic mucosa	UBERON:0000317	97.10	gold quality
esophagus mucosa	UBERON:0002469	97.09	gold quality
skin of abdomen	UBERON:0001416	96.94	gold quality
skin of leg	UBERON:0001511	96.66	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.63	gold quality
small intestine Peyer’s patch	UBERON:0003454	96.11	gold quality
body of stomach	UBERON:0001161	96.02	gold quality
esophagus	UBERON:0001043	95.98	gold quality
gall bladder	UBERON:0002110	95.95	gold quality
large intestine	UBERON:0000059	95.60	gold quality
colon	UBERON:0001155	95.60	gold quality
lower esophagus	UBERON:0013473	95.08	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.06	gold quality
small intestine	UBERON:0002108	95.03	gold quality
intestine	UBERON:0000160	94.85	gold quality
zone of skin	UBERON:0000014	94.79	gold quality
anterior cingulate cortex	UBERON:0009835	94.48	gold quality
right lobe of thyroid gland	UBERON:0001119	94.35	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.29	gold quality
pancreatic ductal cell	CL:0002079	94.26	silver quality
minor salivary gland	UBERON:0001830	94.22	gold quality
left lobe of thyroid gland	UBERON:0001120	93.85	gold quality
right frontal lobe	UBERON:0002810	93.64	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.64	gold quality
amygdala	UBERON:0001876	93.43	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-MTAB-9388	yes	1153.08
E-GEOD-125970	yes	1046.72
E-HCAD-13	yes	169.11
E-MTAB-8410	yes	49.25
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting TMEM54, 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-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-6507-3P	99.35	67.32	1059
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-5587-5P	99.07	68.58	838
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-26B-3P	98.71	67.49	1102
HSA-MIR-6776-5P	98.54	67.43	1304
HSA-MIR-3184-3P	96.96	66.91	845
HSA-MIR-1293	96.16	64.69	916
HSA-MIR-3677-5P	93.16	64.62	393
HSA-MIR-6749-5P	89.28	58.87	75

Literature-anchored findings (GeneRIF, showing 1)

• MicroRNA-148a-3p suppresses the glycolysis and Cell proliferation by targeting transmembrane protein 54 in liver cancer. (PMID:38169186)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem54b	ENSDARG00000035875
danio_rerio	tmem54a	ENSDARG00000059247
mus_musculus	Tmem54	ENSMUSG00000028786
rattus_norvegicus	Tmem54	ENSRNOG00000024259

Paralogs (1): KRTCAP3 (ENSG00000157992)

Protein

Protein identifiers

Transmembrane protein 54 — Q969K7 (reviewed: Q969K7)

Alternative names: Beta-casein-like protein, Protein CAC-1

All UniProt accessions (1): Q969K7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Ubiquitously expressed in cancer cell lines.

Similarity. Belongs to the TMEM54 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q969K7-1	1	yes
Q969K7-2	2
Q969K7-3	3

RefSeq proteins (5): NP_001316651, NP_001316652, NP_001316653, NP_001316654, NP_277039* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR020977	Beta-casein-like	Family

Pfam: PF12304

UniProt features (10 total): transmembrane region 4, splice variant 2, sequence conflict 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q969K7-F1	77.36	0.47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 76 (showing top): BENPORATH_ES_WITH_H3K27ME3, NRF2_Q4, ATF4_Q2, ACTTTAT_MIR1425P, DOUGLAS_BMI1_TARGETS_UP, CERVERA_SDHB_TARGETS_1_UP, chr1p35, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN, NFAT_Q6, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MEISSNER_BRAIN_HCP_WITH_H3K27ME3, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, CHICAS_RB1_TARGETS_SENESCENT, KOHOUTEK_CCNT2_TARGETS, LIM_MAMMARY_STEM_CELL_DN

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

786 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM54	TMEM92	Q6UXU6	433
TMEM54	GAL3ST1	Q99999	405
TMEM54	TMEM134	Q9H6X4	401
TMEM54	KRABD2	Q6ZNG9	393
TMEM54	ZNF518B	Q9C0D4	381
TMEM54	SERF2	P84101	373
TMEM54	ZNF506	Q5JVG8	370
TMEM54	TMEM126B	Q8IUX1	359
TMEM54	SLC16A5	O15375	352
TMEM54	TSEN34	Q9BSV6	351
TMEM54	PRSS35	Q8N3Z0	349
TMEM54	TSPAN15	O95858	341
TMEM54	TSPYL5	Q86VY4	338
TMEM54	TMEM101	Q96IK0	338
TMEM54	BPIFB6	Q8NFQ5	327

IntAct

79 interactions, top by confidence:

A	B	Type	Score
TMEM54	GPR37L1	psi-mi:“MI:0915”(physical association)	0.560
TMEM54		psi-mi:“MI:0915”(physical association)	0.560
KLRC1	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TMEM54	MS4A14	psi-mi:“MI:0915”(physical association)	0.560
NRG1	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TMEM54	SLC12A7	psi-mi:“MI:0915”(physical association)	0.560
ARL13B	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TMEM52B	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
GPR37L1	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TSPO2	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TMEM54	SLC39A2	psi-mi:“MI:0915”(physical association)	0.560
UPK1B	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
PVR	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TMEM54	TIMMDC1	psi-mi:“MI:0915”(physical association)	0.560
	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
GPR152	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
KCNJ8	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TMEM54	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
CD3G	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TMEM54	CLSTN3	psi-mi:“MI:0915”(physical association)	0.560
KCNK5	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
TMEM54	PRPH	psi-mi:“MI:0915”(physical association)	0.560
TMEM54	YWHAG	psi-mi:“MI:0915”(physical association)	0.560
TMEM54	SETDB1	psi-mi:“MI:0915”(physical association)	0.560
KAT5	TMEM54	psi-mi:“MI:0915”(physical association)	0.560
LMO3	TMEM54	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (29): TMEM54 (Two-hybrid), TMEM54 (Two-hybrid), TMEM54 (Two-hybrid), TMEM54 (Two-hybrid), TMEM54 (Two-hybrid), TMEM54 (Two-hybrid), TMEM54 (Two-hybrid), TMEM54 (Two-hybrid), TMEM54 (Two-hybrid), KLRC1 (Two-hybrid), CLSTN3 (Two-hybrid), NRG1 (Two-hybrid), CD3G (Two-hybrid), KCNK5 (Two-hybrid), TMEM52B (Two-hybrid)

ESM2 similar proteins: A0A1D5NY17, A4IF75, B2RVY9, B3SHH9, F6V1J6, O42281, O70578, P19518, P97707, Q06432, Q08CE6, Q08DE1, Q0D289, Q0V9E0, Q14714, Q2MJQ7, Q4R4Z3, Q4V922, Q5CZV0, Q5PRC1, Q5RDV7, Q5XGU1, Q62147, Q66IV3, Q68FV0, Q6AZD1, Q6P0C6, Q6R5J2, Q6ZP80, Q6ZUX7, Q7ZZL8, Q86WI0, Q8BGA2, Q8NBL3, Q8VHW3, Q8VHW4, Q8VHW7, Q8VHW8, Q91Y55, Q925N4

Diamond homologs: Q3SZ72, Q3ZCD2, Q494T4, Q497B3, Q53RY4, Q8K177, Q969K7, Q9D7S1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	43
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
814067	GRCh37/hg19 1p35.2-35.1(chr1:30819875-34380419)x3	Likely pathogenic

SpliceAI

1117 predictions. Top by Δscore:

Variant	Effect	Δscore
1:32895298:AACTT:A	donor_loss	1.0000
1:32895299:ACTTA:A	donor_loss	1.0000
1:32895300:CTTAC:C	donor_loss	1.0000
1:32895301:TTA:T	donor_loss	1.0000
1:32895302:TAC:T	donor_loss	1.0000
1:32895303:A:AC	donor_gain	1.0000
1:32895303:A:T	donor_loss	1.0000
1:32895304:C:A	donor_loss	1.0000
1:32895304:C:CT	donor_gain	1.0000
1:32895304:CCA:C	donor_gain	1.0000
1:32895438:CT:C	acceptor_gain	1.0000
1:32895440:C:CC	acceptor_gain	1.0000
1:32895449:A:C	acceptor_gain	1.0000
1:32895551:TCA:T	donor_loss	1.0000
1:32895552:CA:C	donor_loss	1.0000
1:32895553:A:AC	donor_gain	1.0000
1:32895554:C:CC	donor_gain	1.0000
1:32895554:C:CT	donor_loss	1.0000
1:32895554:CATAA:C	donor_gain	1.0000
1:32898125:CCA:C	donor_gain	1.0000
1:32894946:C:CT	acceptor_gain	0.9900
1:32894947:G:T	acceptor_gain	0.9900
1:32895303:AC:A	donor_gain	0.9900
1:32895304:CC:C	donor_gain	0.9900
1:32895304:CCAT:C	donor_gain	0.9900
1:32895304:CCATG:C	donor_gain	0.9900
1:32895440:CTGCG:C	acceptor_loss	0.9900
1:32895448:C:CT	acceptor_gain	0.9900
1:32895449:A:AC	acceptor_gain	0.9900
1:32895547:GTAC:G	donor_loss	0.9900

AlphaMissense

1412 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:32895573:G:C	F147L	0.971
1:32895573:G:T	F147L	0.971
1:32895575:A:G	F147L	0.971
1:32895431:G:C	S156R	0.965
1:32895431:G:T	S156R	0.965
1:32895433:T:G	S156R	0.965
1:32898243:G:C	S31R	0.961
1:32898243:G:T	S31R	0.961
1:32898245:T:G	S31R	0.961
1:32895421:A:G	W160R	0.952
1:32895421:A:T	W160R	0.952
1:32895720:G:C	S98R	0.941
1:32895720:G:T	S98R	0.941
1:32895722:T:G	S98R	0.941
1:32898240:G:C	F32L	0.935
1:32898240:G:T	F32L	0.935
1:32898242:A:G	F32L	0.935
1:32895956:C:T	G75D	0.924
1:32898282:C:A	M18I	0.920
1:32898282:C:G	M18I	0.920
1:32898282:C:T	M18I	0.920
1:32895726:G:C	S96R	0.915
1:32895726:G:T	S96R	0.915
1:32895728:T:G	S96R	0.915
1:32898253:C:T	G28D	0.914
1:32895574:A:C	F147C	0.906
1:32898254:C:G	G28R	0.904
1:32898153:G:C	N61K	0.902
1:32898153:G:T	N61K	0.902
1:32895427:A:G	C158R	0.898

dbSNP variants (sampled 300 via entrez): RS1000584988 (1:32898055 G>A), RS1000960075 (1:32895089 C>G), RS1001058557 (1:32901885 G>C), RS1001110439 (1:32901223 C>A,T), RS1001250472 (1:32900959 G>A,C), RS1001636297 (1:32897661 T>C), RS1001688400 (1:32901317 C>T), RS1002116319 (1:32903083 T>G), RS1002367886 (1:32896309 G>T), RS1002570188 (1:32899451 G>C), RS1002580494 (1:32902860 A>G), RS1002932117 (1:32902223 GGCAGA>G), RS1003360956 (1:32902639 G>A), RS1003369436 (1:32895742 C>T), RS1004802376 (1:32894746 C>T)

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

1 associations (top):

Study	Trait	p-value
GCST009066_2	Mosaic loss of chromosome Y (Y chromosome dosage)	4.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007783	mosaic loss of chromosome Y measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	7
sodium arsenite	increases expression	3
Cyclosporine	decreases expression, increases expression	2
fluorene-9-bisphenol	decreases expression	1
lead acetate	increases expression	1
cupric chloride	increases expression	1
isobutyl alcohol	increases expression, affects cotreatment, increases abundance	1
pentanal	increases expression	1
dinophysistoxin 1	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	increases 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
Decitabine	affects expression	1
Acetaminophen	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	affects expression	1
Diethylstilbestrol	increases expression	1
Doxorubicin	decreases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Ketoconazole	affects expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Quercetin	increases expression	1
Rotenone	increases expression	1
Smoke	decreases expression	1

Clinical trials (associated diseases)

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