MUCL1

Summary

MUCL1 (mucin like 1, HGNC:30588) is a protein-coding gene on chromosome 12q13.2, encoding Mucin-like protein 1 (Q96DR8). May play a role as marker for the diagnosis of metastatic breast cancer.

Predicted to be located in Golgi lumen and plasma membrane.

Source: NCBI Gene 118430 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_058173

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30588
Approved symbol	MUCL1
Name	mucin like 1
Location	12q13.2
Locus type	gene with protein product
Status	Approved
Aliases	SBEM
Ensembl gene	ENSG00000172551
Ensembl biotype	protein_coding
OMIM	610857
Entrez	118430

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000308796, ENST00000546809, ENST00000547958, ENST00000547990, ENST00000652289

RefSeq mRNA: 1 — MANE Select: NM_058173 NM_058173

CCDS: CCDS8885

Canonical transcript exons

ENST00000308796 — 4 exons

Exon	Start	End
ENSE00001187036	54858193	54858387
ENSE00002412956	54854516	54854640
ENSE00003464798	54856770	54856892
ENSE00003470026	54855116	54855157

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 99.90.

FANTOM5 (CAGE): breadth broad, TPM avg 9.2893 / max 3277.2558, expressed in 220 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125944	7.1272	210
125938	0.6188	5
125940	0.5739	6
125941	0.3748	7
125937	0.2816	5
125942	0.1508	5
125939	0.0956	4
125936	0.0367	3
206733	0.0243	6
125943	0.0055	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper leg skin	UBERON:0004262	99.90	gold quality
parotid gland	UBERON:0001831	99.77	gold quality
skin of hip	UBERON:0001554	99.60	gold quality
skin of leg	UBERON:0001511	98.28	gold quality
mammary duct	UBERON:0001765	97.89	gold quality
nipple	UBERON:0002030	97.81	gold quality
zone of skin	UBERON:0000014	97.63	gold quality
skin of abdomen	UBERON:0001416	96.69	gold quality
thoracic mammary gland	UBERON:0005200	92.39	gold quality
mammary gland	UBERON:0001911	92.31	gold quality
nasal cavity epithelium	UBERON:0005384	91.84	gold quality
mammalian vulva	UBERON:0000997	89.01	gold quality
bronchial epithelial cell	CL:0002328	77.83	silver quality
bronchus	UBERON:0002185	77.71	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	77.63	gold quality
trachea	UBERON:0003126	72.93	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.17	gold quality
nasal cavity mucosa	UBERON:0001826	71.91	gold quality
saliva-secreting gland	UBERON:0001044	70.11	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	69.73	gold quality
right uterine tube	UBERON:0001302	66.84	gold quality
epithelium of nasopharynx	UBERON:0001951	64.91	silver quality
minor salivary gland	UBERON:0001830	62.39	gold quality
right frontal lobe	UBERON:0002810	61.58	gold quality
anterior cingulate cortex	UBERON:0009835	60.26	gold quality
gastrocnemius	UBERON:0001388	60.17	gold quality
mouth mucosa	UBERON:0003729	59.82	gold quality
granulocyte	CL:0000094	59.75	gold quality
right adrenal gland cortex	UBERON:0035827	59.58	gold quality
putamen	UBERON:0001874	58.19	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-75688	yes	1764.26
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): POU2F1, POU2F2

miRNA regulators (miRDB)

9 targeting MUCL1, 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-513A-5P	100.00	69.77	2465
HSA-MIR-1303	99.65	69.77	1662
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-6828-5P	99.31	69.21	1433
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-10526-3P	97.86	64.97	1342
HSA-MIR-3920	97.75	69.02	1168
HSA-MIR-6808-3P	94.13	65.24	516

Literature-anchored findings (GeneRIF, showing 11)

• identification as possible new breast tumor biomarker (PMID:15684711)
• octamer-binding transcription factors participate in the strong expression of SBEM gene in breast tissues (PMID:16720387)
• SBEM may identify a unique subset of breast cancers with poor prognosis and have implications for therapeutic management. (PMID:18269587)
• results demonstrate that SBEM mRNA may be an important marker for targeting breast cancer micrometastasis (PMID:18497056)
• The SBEM might a suitable marker for molecular detection of ITCs in BM in breast cancer patients. Analysis of prognostic value for SBEM mRNA-based assay should take into account the heterogeneity and different molecular subtypes of breast cancer. (PMID:19221791)
• SBEM has the potential to be a specific marker for predicting hematogenous micrometastasis and response to neoadjuvant chemotherapy in breast cancer. (PMID:20364301)
• an important role for MUCL1 in the proliferation of breast cancer cells (PMID:26725324)
• Small breast epithelial mucin promotes the invasion and metastasis of breast cancer cells via promoting epithelialtomesenchymal transition. (PMID:32627029)
• The mucin protein MUCL1 regulates melanogenesis and melanoma genes in a manner dependent on threonine content. (PMID:34545566)
• Targeting MUCL1 protein inhibits cell proliferation and EMT by deregulating betacatenin and increases irinotecan sensitivity in colorectal cancer. (PMID:35059735)
• miRNA-186-5p inhibits migration, invasion and proliferation of breast cancer cells by targeting SBEM. (PMID:37477531)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG13965	FBGN0032834

Protein

Protein identifiers

Mucin-like protein 1 — Q96DR8 (reviewed: Q96DR8)

Alternative names: Protein BS106, Small breast epithelial mucin

All UniProt accessions (2): Q96DR8, F8VV13

UniProt curated annotations — full annotation on UniProt →

Function. May play a role as marker for the diagnosis of metastatic breast cancer.

Subcellular location. Secreted. Membrane.

Tissue specificity. Expressed in mammary, salivary glands and prostate. Also detected in lung. Mainly expressed in cancer cell lines of breast origin. Highly expressed in lymph node-positive compared with node-negative tumors. Detected in all lymph node containing metastatic cells.

Post-translational modifications. O-glycosylated.

Polymorphism. The number of repeats varies from 3 to 2 in one variant form which is equally present in breast cancer tumors.

RefSeq proteins (1): NP_477521* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR054050	MUCL1	Family

Pfam: PF21823

UniProt features (27 total): glycosylation site 17, repeat 3, region of interest 2, compositionally biased region 2, signal peptide 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96DR8-F1	68.01	0.18

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 (17): 24, 30, 34, 46, 47, 51, 52, 54, 55, 59, 60, 62, 63, 66, 67, 68, 23

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

ID	Pathway
R-HSA-5083625	Defective GALNT3 causes HFTC
R-HSA-5083632	Defective C1GALT1C1 causes TNPS
R-HSA-5083636	Defective GALNT12 causes CRCS1
R-HSA-5621480	Dectin-2 family
R-HSA-913709	O-linked glycosylation of mucins
R-HSA-977068	Termination of O-glycan biosynthesis
R-HSA-1643685	Disease
R-HSA-168249	Innate Immune System
R-HSA-168256	Immune System
R-HSA-3781865	Diseases of glycosylation
R-HSA-3906995	Diseases associated with O-glycosylation of proteins
R-HSA-392499	Metabolism of proteins
R-HSA-5173105	O-linked glycosylation
R-HSA-5621481	C-type lectin receptors (CLRs)
R-HSA-5668914	Diseases of metabolism
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 55 (showing top): REACTOME_INNATE_IMMUNE_SYSTEM, GOZGIT_ESR1_TARGETS_DN, TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN, MODULE_48, MODULE_95, RICKMAN_HEAD_AND_NECK_CANCER_C, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, GOCC_GOLGI_LUMEN, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, MODULE_163, REACTOME_DISEASES_OF_GLYCOSYLATION, REACTOME_DISEASES_ASSOCIATED_WITH_O_GLYCOSYLATION_OF_PROTEINS, REACTOME_DEFECTIVE_GALNT3_CAUSES_HFTC

GO Biological Process (0):

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

GO Cellular Component (4): extracellular region (GO:0005576), Golgi lumen (GO:0005796), plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-11 pathways:

Category	Pathways
Diseases associated with O-glycosylation of proteins	3
C-type lectin receptors (CLRs)	1
O-linked glycosylation	1
O-linked glycosylation of mucins	1
Immune System	1
Diseases of metabolism	1
Diseases of glycosylation	1
Post-translational protein modification	1
Innate Immune System	1
Disease	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
Golgi apparatus	1
intracellular organelle lumen	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

652 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MUCL1	SCGB2A2	Q13296	944
MUCL1	SCGB1D2	O95969	482
MUCL1	GLYATL2	Q8WU03	477
MUCL1	C5orf46	Q6UWT4	445
MUCL1	IGF2BP3	O00425	416
MUCL1	NEDD9	Q14511	389
MUCL1	ZNF232	Q9UNY5	348
MUCL1	MAP7	Q14244	341
MUCL1	WFDC5	Q8TCV5	314
MUCL1	CHID1	Q9BWS9	313
MUCL1	ADGRF4	Q8IZF3	301
MUCL1	TESPA1	A2RU30	296
MUCL1	SUSD3	Q96L08	296
MUCL1	PPP4R4	Q6NUP7	294
MUCL1	PIP	P12273	290

IntAct

42 interactions, top by confidence:

A	B	Type	Score
KHDRBS2	KHDRBS3	psi-mi:“MI:0914”(association)	0.800
HEXIM2	AHCYL1	psi-mi:“MI:0914”(association)	0.740
MUCL1	PDIA5	psi-mi:“MI:0914”(association)	0.640
CEP72	AHCYL1	psi-mi:“MI:0914”(association)	0.640
ARL13B	MUCL1	psi-mi:“MI:0915”(physical association)	0.560
GARRE1	APOD	psi-mi:“MI:0914”(association)	0.530
DHX57	APOD	psi-mi:“MI:0914”(association)	0.530
MTHFD2L	MTHFD2	psi-mi:“MI:0914”(association)	0.530
KLHL10	PXDNL	psi-mi:“MI:0914”(association)	0.530
ERBB2	MUCL1	psi-mi:“MI:0915”(physical association)	0.370
RNLS	STATH	psi-mi:“MI:0914”(association)	0.350
ATP2B2	GPR89A	psi-mi:“MI:0914”(association)	0.350
ARHGAP36		psi-mi:“MI:0914”(association)	0.350
HVCN1	DOK2	psi-mi:“MI:0914”(association)	0.350
SPACA9	RIOX2	psi-mi:“MI:0914”(association)	0.350
SEPTIN8	RIOK3	psi-mi:“MI:0914”(association)	0.350
ATP2B2	ESYT2	psi-mi:“MI:0914”(association)	0.350
PTCH1	PLXNB2	psi-mi:“MI:0914”(association)	0.350
ARHGAP36	PJA2	psi-mi:“MI:0914”(association)	0.350
SLC38A6	EDIL3	psi-mi:“MI:0914”(association)	0.350
TLR1	LRP6	psi-mi:“MI:0914”(association)	0.350
ZNF451	HERC2	psi-mi:“MI:0914”(association)	0.350
DHX57	H2AC4	psi-mi:“MI:0914”(association)	0.350
GK3	APOD	psi-mi:“MI:0914”(association)	0.350
CYP4F8	APOD	psi-mi:“MI:0914”(association)	0.350
OR1E1	EMC4	psi-mi:“MI:0914”(association)	0.350
SCGB1D1	IGLL5	psi-mi:“MI:0914”(association)	0.350

BioGRID (43): MUCL1 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), MUCL1 (Two-hybrid), PDIA5 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), EMC4 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS), MUCL1 (Affinity Capture-MS)

ESM2 similar proteins: A0A024QYT3, A0A088SG62, A0A182RFI2, A0A6G9KHE4, A0A6M3Z9I6, A1L019, A7RJ12, A8WUV8, A8X7F0, A8XYS0, A8Y181, B0XTU6, B3EX01, B6DDU5, D0MSS2, K7NTD0, K9J977, O61704, P0DPX0, P0DRA3, P0DRA4, P0DSK3, P0DY55, P14199, P21250, P34472, P40148, P59704, P68408, P68409, P86146, P86718, P86719, P91859, Q09416, Q1EG28, Q21175, Q21771, Q24629, Q27913

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

322 predictions. Top by Δscore:

Variant	Effect	Δscore
12:54854613:G:GT	donor_gain	1.0000
12:54854636:TGCCC:T	donor_gain	1.0000
12:54854637:GCCC:G	donor_gain	1.0000
12:54854637:GCCCG:G	donor_gain	1.0000
12:54854638:CCC:C	donor_gain	1.0000
12:54854639:CC:C	donor_gain	1.0000
12:54854641:G:GA	donor_loss	1.0000
12:54854641:G:GG	donor_gain	1.0000
12:54854642:T:TC	donor_loss	1.0000
12:54854645:G:GG	donor_gain	1.0000
12:54855154:GCTA:G	donor_gain	1.0000
12:54855158:G:GG	donor_gain	1.0000
12:54856762:A:AG	acceptor_gain	1.0000
12:54856763:A:G	acceptor_gain	1.0000
12:54856767:CAG:C	acceptor_loss	1.0000
12:54856768:A:AC	acceptor_loss	1.0000
12:54856768:A:AG	acceptor_gain	1.0000
12:54856768:AGCT:A	acceptor_gain	1.0000
12:54856769:G:GA	acceptor_gain	1.0000
12:54856769:GCT:G	acceptor_gain	1.0000
12:54856769:GCTG:G	acceptor_gain	1.0000
12:54854643:AA:A	donor_loss	0.9900
12:54855110:TTTCA:T	acceptor_loss	0.9900
12:54855112:TCAGA:T	acceptor_loss	0.9900
12:54855113:CA:C	acceptor_loss	0.9900
12:54855114:A:AG	acceptor_gain	0.9900
12:54855115:G:GG	acceptor_gain	0.9900
12:54855115:G:T	acceptor_loss	0.9900
12:54855115:GA:G	acceptor_gain	0.9900
12:54855115:GAGA:G	acceptor_gain	0.9900

AlphaMissense

559 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:54854613:G:A	G11R	0.979
12:54854613:G:C	G11R	0.979
12:54854614:G:A	G11E	0.955
12:54854605:T:A	V8E	0.934
12:54854596:C:A	A5E	0.932
12:54854617:T:A	V12D	0.922
12:54854599:T:A	V6D	0.912
12:54854608:T:A	L9H	0.908
12:54854608:T:G	L9R	0.897
12:54854589:T:C	F3L	0.887
12:54854591:C:A	F3L	0.887
12:54854591:C:G	F3L	0.887
12:54854602:T:G	L7R	0.822
12:54854632:T:A	V17D	0.807
12:54854608:T:C	L9P	0.803
12:54858206:G:C	W79C	0.787
12:54858206:G:T	W79C	0.787
12:54854587:A:T	K2M	0.780
12:54854602:T:A	L7Q	0.780
12:54858204:T:A	W79R	0.774
12:54858204:T:C	W79R	0.774
12:54854586:A:G	K2E	0.765
12:54854588:G:C	K2N	0.761
12:54854588:G:T	K2N	0.761
12:54854629:T:C	L16P	0.701
12:54854593:T:C	L4S	0.677
12:54854625:T:C	F15L	0.666
12:54854627:T:A	F15L	0.666
12:54854627:T:G	F15L	0.666
12:54854629:T:G	L16R	0.666

dbSNP variants (sampled 300 via entrez): RS1000076458 (12:54848481 T>C), RS1000390893 (12:54836920 T>C), RS1000409203 (12:54845646 T>A,C), RS1000461001 (12:54845946 A>G,T), RS1000665805 (12:54841141 C>T), RS1000751520 (12:54852237 C>T), RS1000755911 (12:54840389 A>C), RS1000772365 (12:54836082 G>A,C), RS1000935613 (12:54830985 G>A,T), RS1000992889 (12:54835568 T>A), RS1001001712 (12:54830258 GTCTC>G,GTC,GTCTCTC), RS1001015388 (12:54840844 G>A), RS1001035111 (12:54845163 G>C,T), RS1001132759 (12:54848196 G>C), RS1001284306 (12:54830667 T>C)

Disease associations

OMIM: gene MIM:610857 | 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
GCST007995_38	Asthma (childhood onset)	1.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	2
methyleugenol	decreases expression	1
sodium arsenate	decreases expression, increases abundance	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic	decreases expression, increases abundance	1
Estradiol	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Rotenone	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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