SECTM1

Summary

SECTM1 (secreted and transmembrane 1, HGNC:10707) is a protein-coding gene on chromosome 17q25.3, encoding Secreted and transmembrane protein 1 (Q8WVN6). May be involved in thymocyte signaling.

This gene encodes a transmembrane and secreted protein with characteristics of a type 1a transmembrane protein. It is found in a perinuclear Golgi-like pattern and thought to be involved in hematopoietic and/or immune system processes.

Source: NCBI Gene 6398 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 51 total
• MANE Select transcript: NM_003004

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10707
Approved symbol	SECTM1
Name	secreted and transmembrane 1
Location	17q25.3
Locus type	gene with protein product
Status	Approved
Aliases	K12
Ensembl gene	ENSG00000141574
Ensembl biotype	protein_coding
OMIM	602602
Entrez	6398

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 18 protein_coding, 1 nonsense_mediated_decay

ENST00000269389, ENST00000580437, ENST00000581691, ENST00000581864, ENST00000581954, ENST00000582290, ENST00000582563, ENST00000583093, ENST00000856789, ENST00000856790, ENST00000856791, ENST00000856792, ENST00000856793, ENST00000856794, ENST00000856795, ENST00000856796, ENST00000856797, ENST00000927831, ENST00000958226

RefSeq mRNA: 1 — MANE Select: NM_003004 NM_003004

CCDS: CCDS11808

Canonical transcript exons

ENST00000269389 — 5 exons

Exon	Start	End
ENSE00000949847	82324582	82324890
ENSE00001243873	82321024	82322370
ENSE00001309259	82327147	82327292
ENSE00002704588	82333700	82333766
ENSE00003660290	82322878	82323011

Expression profiles

Bgee: expression breadth ubiquitous, 229 present calls, max score 98.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.2013 / max 933.6635, expressed in 1044 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
168978	6.2072	681
168979	5.9650	868
168981	0.8516	333
168980	0.0934	47
168977	0.0840	28

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	98.03	gold quality
mononuclear cell	CL:0000842	98.00	gold quality
leukocyte	CL:0000738	97.92	gold quality
granulocyte	CL:0000094	97.18	gold quality
blood	UBERON:0000178	96.20	gold quality
mucosa of transverse colon	UBERON:0004991	94.99	gold quality
ileal mucosa	UBERON:0000331	94.14	gold quality
jejunal mucosa	UBERON:0000399	93.25	gold quality
duodenum	UBERON:0002114	93.23	gold quality
spleen	UBERON:0002106	90.91	gold quality
vermiform appendix	UBERON:0001154	90.75	gold quality
decidua	UBERON:0002450	88.58	gold quality
small intestine	UBERON:0002108	88.56	gold quality
small intestine Peyer’s patch	UBERON:0003454	88.40	gold quality
transverse colon	UBERON:0001157	87.87	gold quality
rectum	UBERON:0001052	87.77	gold quality
nasal cavity epithelium	UBERON:0005384	87.55	gold quality
minor salivary gland	UBERON:0001830	87.43	gold quality
caecum	UBERON:0001153	87.08	gold quality
pancreatic ductal cell	CL:0002079	86.41	silver quality
gall bladder	UBERON:0002110	86.20	gold quality
mouth mucosa	UBERON:0003729	86.10	gold quality
omental fat pad	UBERON:0010414	85.79	gold quality
peritoneum	UBERON:0002358	85.73	gold quality
saliva-secreting gland	UBERON:0001044	85.69	gold quality
upper lobe of left lung	UBERON:0008952	85.65	gold quality
intestine	UBERON:0000160	85.64	gold quality
colon	UBERON:0001155	85.62	gold quality
large intestine	UBERON:0000059	85.34	gold quality
adipose tissue of abdominal region	UBERON:0007808	85.06	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.31
E-MTAB-8498	yes	10.41
E-GEOD-99795	no	78.22
E-MTAB-4850	no	43.01

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NFKB, STAT3

miRNA regulators (miRDB)

16 targeting SECTM1, 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-4283	100.00	66.42	2097
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-4260	98.78	65.37	848
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-890	97.47	68.67	982
HSA-MIR-134-3P	96.83	66.22	1001
HSA-MIR-1226-5P	96.50	65.28	643
HSA-MIR-6874-5P	95.73	64.94	545
HSA-MIR-103B	95.51	66.85	441
HSA-MIR-4633-3P	93.85	63.56	534
HSA-MIR-6500-5P	93.85	63.64	522
HSA-MIR-4785	88.53	62.71	63
HSA-MIR-658	88.20	67.03	178
HSA-MIR-4783-3P	73.56	61.87	82

Literature-anchored findings (GeneRIF, showing 4)

• level of SECTM1 expression is likely to be a key factor in innate immune responses and in the immune tolerance of cancerous cells (PMID:21749909)
• CD7 is present on monocytes and tumor macrophages and its ligand, SECTM1, is frequently expressed in corresponding melanoma tissues (PMID:24157461)
• SECTM1 secreted from bone marrow stromal cells may interact with CD7 to influence GM-CSF expression in leukemic cells. (PMID:24211252)
• SECTM1 promotes the development of glioblastoma and mesenchymal transition by regulating the TGFbeta1/Smad signaling pathway. (PMID:38164182)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Sectm1a	ENSMUSG00000025165
mus_musculus	Sectm1b	ENSMUSG00000039364
rattus_norvegicus	Sectm1a	ENSRNOG00000036672
rattus_norvegicus	Sectm1b	ENSRNOG00000036673

Protein

Protein identifiers

Secreted and transmembrane protein 1 — Q8WVN6 (reviewed: Q8WVN6)

Alternative names: Protein K-12

All UniProt accessions (8): Q8WVN6, J3KS40, J3KSN0, J3KTR4, J3QKK2, J3QQU6, J3QR99, J3QRU5

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in thymocyte signaling.

Subunit / interactions. Interacts with CD7.

Subcellular location. Cell membrane. Secreted.

Tissue specificity. Detected at the highest levels in peripheral blood leukocytes and breast cancer cell lines. Found in leukocytes of the myeloid lineage, with the strongest expression observed in granulocytes and no detectable expression in lymphocytes. Expressed in thymic epithelial cells and fibroblasts.

Induction. By IFNG/IFN-gamma (at protein level).

Similarity. Belongs to the SECTM family.

RefSeq proteins (1): NP_002995* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013783	Ig-like_fold	Homologous_superfamily
IPR033231	SECTM1	Family

UniProt features (8 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1, glycosylation site 1, disulfide bond 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
12NP	X-RAY DIFFRACTION	2.4

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WVN6-F1	75.00	0.43

Functional residue map

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

Disulfide bonds (1): 38–55

Glycosylation sites (1): 56

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 256 (showing top): WALLACE_PROSTATE_CANCER_RACE_UP, GOBP_POSITIVE_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, BENPORATH_ES_WITH_H3K27ME3, GOBP_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION_INVOLVED_IN_IMMUNE_RESPONSE, MODULE_45, MODULE_418, GOZGIT_ESR1_TARGETS_DN, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, GOBP_REGULATION_OF_IMMUNE_RESPONSE, RICKMAN_METASTASIS_DN, GOBP_LYMPHOCYTE_MEDIATED_IMMUNITY, FOSTER_TOLERANT_MACROPHAGE_UP

GO Biological Process (6): positive regulation of T cell cytokine production (GO:0002726), immune response (GO:0006955), mesoderm development (GO:0007498), positive regulation of canonical NF-kappaB signal transduction (GO:0043123), signal transduction (GO:0007165), interleukin-2-mediated signaling pathway (GO:0038110)

GO Molecular Function (3): cytokine activity (GO:0005125), receptor ligand activity (GO:0048018), protein binding (GO:0005515)

GO Cellular Component (6): obsolete extracellular space (GO:0005615), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), membrane (GO:0016020), extracellular exosome (GO:0070062), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
T cell cytokine production	1
positive regulation of T cell mediated immunity	1
positive regulation of cytokine production involved in immune response	1
regulation of T cell cytokine production	1
immune system process	1
response to stimulus	1
tissue development	1
canonical NF-kappaB signal transduction	1
regulation of canonical NF-kappaB signal transduction	1
positive regulation of intracellular signal transduction	1
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
cytokine-mediated signaling pathway	1
cellular response to interleukin-2	1
receptor ligand activity	1
signaling receptor binding	1
signal transduction	1
signaling receptor activator activity	1
binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
extracellular vesicle	1

Protein interactions and networks

STRING

508 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SECTM1	CD7	P09564	951
SECTM1	TEX19	Q8NA77	462
SECTM1	KRT12	Q99456	399
SECTM1	KRT33B	Q14525	377
SECTM1	ZNF664	Q8N3J9	374
SECTM1	KRT34	O76011	364
SECTM1	ZMYND15	Q9H091	327
SECTM1	IGFLR1	Q9H665	322
SECTM1	PLEKHA4	Q9H4M7	320
SECTM1	HERC2	O95714	318
SECTM1	UBD	O15205	317
SECTM1	GPR162	Q16538	311
SECTM1	IPP	Q9Y573	307
SECTM1	SINHCAF	Q9NP50	305
SECTM1	TMIGD1	Q6UXZ0	303

IntAct

14 interactions, top by confidence:

A	B	Type	Score
ANKRD46	SECTM1	psi-mi:“MI:0915”(physical association)	0.560
EMP3	SECTM1	psi-mi:“MI:0915”(physical association)	0.560
CLEC4A	SEMA7A	psi-mi:“MI:0914”(association)	0.530
NLRP12	SECTM1	psi-mi:“MI:0915”(physical association)	0.370
SECTM1	GAPDHS	psi-mi:“MI:0914”(association)	0.350
CLEC4A		psi-mi:“MI:0914”(association)	0.350
CD7	PIK3R2	psi-mi:“MI:0914”(association)	0.350
RYK	DUSP14	psi-mi:“MI:0914”(association)	0.350
EMP3	SECTM1	psi-mi:“MI:0915”(physical association)	0.000
ANKRD46	SECTM1	psi-mi:“MI:0915”(physical association)	0.000
Y0062	SECTM1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (19): ALDH1B1 (Affinity Capture-MS), BCLAF1 (Affinity Capture-MS), CANX (Affinity Capture-MS), DDX60L (Affinity Capture-MS), DNAJB11 (Affinity Capture-MS), NUP210 (Affinity Capture-MS), PDIA6 (Affinity Capture-MS), SDF2 (Affinity Capture-MS), SDF2L1 (Affinity Capture-MS), SECTM1 (Affinity Capture-MS), SECTM1 (Affinity Capture-MS), EMP3 (Two-hybrid), ANKRD46 (Two-hybrid), GAPDHS (Affinity Capture-MS), CCDC109B (Affinity Capture-MS)

ESM2 similar proteins: A2A7V7, A2TGX5, A5D7B2, O88875, O95866, O95944, O95971, O95998, P22273, Q01114, Q02242, Q1ERP8, Q2LA85, Q2TB54, Q3B8P2, Q3LRV9, Q3U497, Q566E6, Q5R770, Q5T2D2, Q60513, Q63994, Q6DKI7, Q6MG59, Q6QUN5, Q6SJQ0, Q6SJQ5, Q6SJQ7, Q6TYI6, Q6UXG3, Q6UXN2, Q7L513, Q7TSN2, Q86YW5, Q8K558, Q8N109, Q8NHJ6, Q8NHK3, Q8TDQ1, Q8VCH2

Diamond homologs: Q8WVN6, Q921W8, Q9JL59

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1155 predictions. Top by Δscore:

Variant	Effect	Δscore
17:82322371:C:CC	acceptor_gain	1.0000
17:82322873:CCTAC:C	donor_loss	1.0000
17:82322875:TA:T	donor_loss	1.0000
17:82322876:A:AT	donor_loss	1.0000
17:82322877:C:CA	donor_loss	1.0000
17:82322879:T:TA	donor_gain	1.0000
17:82324578:TCA:T	donor_loss	1.0000
17:82324579:CA:C	donor_loss	1.0000
17:82324581:C:G	donor_loss	1.0000
17:82324583:TGAA:T	donor_gain	1.0000
17:82327289:CTCC:C	acceptor_gain	1.0000
17:82322368:CTT:C	acceptor_gain	0.9900
17:82322371:C:A	acceptor_loss	0.9900
17:82322876:ACCT:A	donor_gain	0.9900
17:82322876:ACCTC:A	donor_gain	0.9900
17:82322877:CCTC:C	donor_gain	0.9900
17:82322877:CCTCC:C	donor_gain	0.9900
17:82322880:C:A	donor_gain	0.9900
17:82323106:C:CA	donor_gain	0.9900
17:82324581:CCTG:C	donor_gain	0.9900
17:82324582:CTGA:C	donor_gain	0.9900
17:82324590:T:TA	donor_gain	0.9900
17:82324886:CCAGC:C	acceptor_gain	0.9900
17:82324887:CAGC:C	acceptor_gain	0.9900
17:82324887:CAGCC:C	acceptor_gain	0.9900
17:82324890:CCT:C	acceptor_loss	0.9900
17:82324891:C:CC	acceptor_gain	0.9900
17:82324891:CT:C	acceptor_loss	0.9900
17:82324892:T:C	acceptor_loss	0.9900
17:82324900:C:CT	acceptor_gain	0.9900

AlphaMissense

1595 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:82324634:C:A	W117C	0.998
17:82324634:C:G	W117C	0.998
17:82324636:A:G	W117R	0.996
17:82324636:A:T	W117R	0.996
17:82324751:G:C	F78L	0.994
17:82324751:G:T	F78L	0.994
17:82324753:A:G	F78L	0.994
17:82324821:C:G	C55S	0.994
17:82324822:A:T	C55S	0.994
17:82324680:A:G	L102P	0.993
17:82324712:C:A	W91C	0.993
17:82324712:C:G	W91C	0.993
17:82324821:C:T	C55Y	0.992
17:82324752:A:G	F78S	0.991
17:82324822:A:G	C55R	0.991
17:82324707:A:G	L93P	0.989
17:82324635:C:G	W117S	0.988
17:82324629:A:G	L119P	0.987
17:82324642:A:C	Y115D	0.987
17:82324872:C:G	C38S	0.987
17:82324873:A:T	C38S	0.987
17:82324714:A:G	W91R	0.986
17:82324714:A:T	W91R	0.986
17:82324820:G:C	C55W	0.986
17:82324873:A:G	C38R	0.986
17:82324648:C:A	G113W	0.985
17:82324794:A:T	V64D	0.985
17:82324872:C:T	C38Y	0.985
17:82324616:C:A	Q123H	0.984
17:82324616:C:G	Q123H	0.984

dbSNP variants (sampled 300 via entrez): RS1000048831 (17:82328139 T>A,G), RS1000262018 (17:82331010 C>G), RS1000293046 (17:82330820 G>A), RS1000504797 (17:82334501 C>T), RS1000625091 (17:82335321 T>C), RS1000636898 (17:82329675 G>A,T), RS1000699665 (17:82330891 C>A,G,T), RS1000717352 (17:82326090 C>A), RS1000765462 (17:82324715 G>A), RS1000773316 (17:82330682 G>A,C), RS1001154228 (17:82334134 C>T), RS1001251371 (17:82333343 CAA>C), RS1001324787 (17:82333147 C>A,T), RS1001522182 (17:82334316 G>A), RS1001589682 (17:82326263 G>A,C,T)

Disease associations

OMIM: gene MIM:602602 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006585_879	Blood protein levels	2.000000e-26
GCST90002394_416	Monocyte percentage of white cells	8.000000e-18

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007989	monocyte percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	4
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	3
Tetrachlorodibenzodioxin	increases expression	3
Particulate Matter	decreases expression, increases abundance, increases expression	3
(+)-JQ1 compound	decreases expression	2
Arsenic Trioxide	decreases expression, increases expression	2
Estradiol	affects cotreatment, decreases expression, increases expression	2
Nickel	decreases expression, increases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
GSK-J4	increases expression	1
OTX015	decreases expression	1
mivebresib	decreases expression	1
dicrotophos	decreases expression	1
chloroacetaldehyde	increases expression	1
triphenyl phosphate	affects expression	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
2-methyl-4-isothiazolin-3-one	decreases expression	1
kojic acid	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
perfluorooctanoic acid	decreases expression	1
ferrous chloride	decreases expression	1
aflatoxin B2	decreases methylation	1
nickel sulfate	decreases expression	1
ceric oxide	decreases expression	1
1-nitropyrene	decreases expression	1
cobalt oxide	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
entinostat	increases expression	1
2,2’,4,4’,5-brominated diphenyl ether	increases expression	1
abrine	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1HG	Abcam A-549 SECTM1 KO 2	Cancer cell line	Male
CVCL_B2PZ	Abcam A-549 SECTM1 KO 1	Cancer cell line	Male

Clinical trials (associated diseases)

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