SMCO1

Summary

SMCO1 (single-pass membrane protein with coiled-coil domains 1, HGNC:27407) is a protein-coding gene on chromosome 3q29, encoding Single-pass membrane and coiled-coil domain-containing protein 1 (Q147U7).

Predicted to be located in membrane.

Source: NCBI Gene 255798 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 23 total
• MANE Select transcript: NM_001077657

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27407
Approved symbol	SMCO1
Name	single-pass membrane protein with coiled-coil domains 1
Location	3q29
Locus type	gene with protein product
Status	Approved
Aliases	FLJ41923, DKFZp313B0440
Ensembl gene	ENSG00000214097
Ensembl biotype	protein_coding
Entrez	255798

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay

ENST00000397537, ENST00000452776, ENST00000958040, ENST00000958041

RefSeq mRNA: 2 — MANE Select: NM_001077657 NM_001077657, NM_001320473

CCDS: CCDS43192

Canonical transcript exons

ENST00000397537 — 3 exons

Exon	Start	End
ENSE00001529104	196515160	196515346
ENSE00001911783	196506879	196508331
ENSE00003653888	196509520	196509669

Expression profiles

Bgee: expression breadth broad, 80 present calls, max score 96.84.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.9712 / max 216.0315, expressed in 47 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
46364	0.9167	46
46365	0.0544	21

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
hindlimb stylopod muscle	UBERON:0004252	96.84	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.36	gold quality
deltoid	UBERON:0001476	95.62	gold quality
quadriceps femoris	UBERON:0001377	95.07	gold quality
vastus lateralis	UBERON:0001379	94.94	gold quality
biceps brachii	UBERON:0001507	94.58	gold quality
apex of heart	UBERON:0002098	93.76	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	93.57	gold quality
skeletal muscle tissue	UBERON:0001134	92.51	gold quality
myocardium	UBERON:0002349	90.32	gold quality
heart left ventricle	UBERON:0002084	90.03	gold quality
cardiac ventricle	UBERON:0002082	89.85	gold quality
heart right ventricle	UBERON:0002080	86.44	gold quality
body of tongue	UBERON:0011876	86.27	gold quality
muscle tissue	UBERON:0002385	85.60	gold quality
right atrium auricular region	UBERON:0006631	83.74	gold quality
cardiac atrium	UBERON:0002081	83.38	gold quality
muscle of leg	UBERON:0001383	82.02	gold quality
heart	UBERON:0000948	81.87	gold quality
gastrocnemius	UBERON:0001388	81.19	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.97	gold quality
tongue	UBERON:0001723	72.80	gold quality
tendon of biceps brachii	UBERON:0008188	64.52	gold quality
superior surface of tongue	UBERON:0007371	61.15	gold quality
pharyngeal mucosa	UBERON:0000355	58.35	gold quality
jejunum	UBERON:0002115	56.08	gold quality
lower lobe of lung	UBERON:0008949	53.72	silver quality
buccal mucosa cell	CL:0002336	52.42	gold quality
synovial joint	UBERON:0002217	50.20	silver quality
cerebellar vermis	UBERON:0004720	48.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

67 targeting SMCO1, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-549A-3P	99.54	68.17	825

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smco1	ENSMUSG00000046345
rattus_norvegicus	Smco1	ENSRNOG00000024960

Protein

Protein identifiers

Single-pass membrane and coiled-coil domain-containing protein 1 — Q147U7 (reviewed: Q147U7)

Alternative names: Single-pass membrane protein with coiled-coil domains 1

All UniProt accessions (2): F8WEP5, Q147U7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (2): NP_001071125, NP_001307402 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027875	DUF4547	Family

Pfam: PF15080

UniProt features (5 total): sequence variant 2, chain 1, transmembrane region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q147U7-F1	89.39	0.80

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): CBX7_TARGET_GENES, HDAC4_TARGET_GENES, MEF2D_TARGET_GENES, MIR4495, MIR499A_5P, MIR3158_5P, MIR149_5P, MIR647, MIR4296, MIR3622A_5P, WP_3Q29_COPY_NUMBER_VARIATION_SYNDROME, DESCARTES_MAIN_FETAL_ELF3_AGBL2_POSITIVE_CELLS, GSE29614_CTRL_VS_TIV_FLU_VACCINE_PBMC_2007_UP, GSE29614_CTRL_VS_DAY7_TIV_FLU_VACCINE_PBMC_UP, FONG_MCMASTER_OPA1_CARDIOPROTECTION_UP

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

222 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMCO1	WDR53	Q7Z5U6	751
SMCO1	UBXN7	O94888	690
SMCO1	ZDHHC19	Q8WVZ1	675
SMCO1	DYNLT2B	Q8WW35	649
SMCO1	TM4SF19	Q96DZ7	644
SMCO1	CEP19	Q96LK0	634
SMCO1	TMEM252	Q8N6L7	591
SMCO1	SMR3B	P02814	576
SMCO1	FBXO45	P0C2W1	559
SMCO1	NRROS	Q86YC3	533
SMCO1	PCYT1A	P49585	531
SMCO1	SLC51A	Q86UW1	525
SMCO1	PIGZ	Q86VD9	470
SMCO1	SMCO2	A6NFE2	447
SMCO1	SBK3	P0C264	446

IntAct

13 interactions, top by confidence:

A	B	Type	Score
SMCO1	FNDC8	psi-mi:“MI:0915”(physical association)	0.560
SMCO1	SGK3	psi-mi:“MI:0915”(physical association)	0.490
SMCO1	CREB1	psi-mi:“MI:0915”(physical association)	0.490
SGK3	SMCO1	psi-mi:“MI:0915”(physical association)	0.490
CREB1	SMCO1	psi-mi:“MI:0915”(physical association)	0.490
SMCO1	E4	psi-mi:“MI:0915”(physical association)	0.370
ECE1	SMCO1	psi-mi:“MI:0915”(physical association)	0.370
SMCO1	SPAG9	psi-mi:“MI:0914”(association)	0.350
cpsA	SMCO1	psi-mi:“MI:0914”(association)	0.350
SMCO1	FNDC8	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (8): SPAG9 (Affinity Capture-MS), MAPK8IP3 (Affinity Capture-MS), CREB1 (Two-hybrid), SGK3 (Two-hybrid), SMCO1 (Two-hybrid), SPAG9 (Affinity Capture-MS), MAPK8IP3 (Affinity Capture-MS), SMCO1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2BTD8, A8G763, H2BXL5, O24301, O49845, O83479, P03870, P04712, P06529, P0AEV4, P0AEV5, P0AEV6, P12798, P13708, P13770, P17743, P18688, P30298, P31922, P31923, P31924, P34335, P38265, P39279, P44413, P46018, P46019, P46020, P49034, P49036, Q00124, Q00917, Q09400, Q147U7, Q318I3, Q41608, Q43009, Q50973, Q5ZXN5, Q64649

Diamond homologs: Q147U7, Q8CEZ1

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	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

335 predictions. Top by Δscore:

Variant	Effect	Δscore
3:196509515:CTCA:C	donor_gain	1.0000
3:196509518:A:AC	donor_gain	1.0000
3:196509519:C:CA	donor_gain	1.0000
3:196509519:CT:C	donor_gain	1.0000
3:196509519:CTG:C	donor_gain	1.0000
3:196509519:CTGG:C	donor_gain	1.0000
3:196509519:CTGGA:C	donor_gain	1.0000
3:196509665:CTACT:C	acceptor_gain	1.0000
3:196509666:TACT:T	acceptor_gain	1.0000
3:196509667:ACT:A	acceptor_gain	1.0000
3:196509668:CT:C	acceptor_gain	1.0000
3:196509668:CTC:C	acceptor_gain	1.0000
3:196509669:TCT:T	acceptor_gain	1.0000
3:196509669:TCTGT:T	acceptor_loss	1.0000
3:196509670:C:A	acceptor_loss	1.0000
3:196509670:C:CC	acceptor_gain	1.0000
3:196509670:C:G	acceptor_gain	1.0000
3:196509672:G:C	acceptor_gain	1.0000
3:196508332:C:CC	acceptor_gain	0.9900
3:196509511:GATAC:G	donor_loss	0.9900
3:196509512:ATAC:A	donor_loss	0.9900
3:196509513:TACT:T	donor_loss	0.9900
3:196509514:ACT:A	donor_loss	0.9900
3:196509517:CA:C	donor_loss	0.9900
3:196509518:ACT:A	donor_loss	0.9900
3:196509672:G:GC	acceptor_gain	0.9900
3:196509677:A:AC	acceptor_gain	0.9900
3:196509677:A:C	acceptor_gain	0.9900
3:196508330:GC:G	acceptor_gain	0.9800
3:196508330:GCCTA:G	acceptor_loss	0.9800

AlphaMissense

1410 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:196508298:G:C	S78R	0.976
3:196508298:G:T	S78R	0.976
3:196508300:T:G	S78R	0.976
3:196508168:A:G	W122R	0.962
3:196508168:A:T	W122R	0.962
3:196507987:A:G	L182S	0.951
3:196508227:A:G	L102P	0.944
3:196507979:C:G	A185P	0.937
3:196509542:A:G	W60R	0.930
3:196509542:A:T	W60R	0.930
3:196508166:C:A	W122C	0.918
3:196508166:C:G	W122C	0.918
3:196507989:A:C	S181R	0.916
3:196507989:A:T	S181R	0.916
3:196507991:T:G	S181R	0.916
3:196509633:G:C	F29L	0.914
3:196509633:G:T	F29L	0.914
3:196509635:A:G	F29L	0.914
3:196509604:A:G	L39P	0.911
3:196508140:A:G	L131P	0.910
3:196507978:G:T	A185D	0.909
3:196508106:G:C	F142L	0.908
3:196508106:G:T	F142L	0.908
3:196508108:A:G	F142L	0.908
3:196508209:A:T	V108E	0.907
3:196508248:A:G	L95P	0.901
3:196509540:C:A	W60C	0.896
3:196509540:C:G	W60C	0.896
3:196509591:G:C	F43L	0.879
3:196509591:G:T	F43L	0.879

dbSNP variants (sampled 300 via entrez): RS1000008254 (3:196508171 C>A), RS1000091285 (3:196517482 C>T), RS1000104741 (3:196514302 C>T), RS1001038201 (3:196514284 A>G), RS1001132822 (3:196508445 A>G), RS1001161142 (3:196509156 T>G), RS1001437977 (3:196508696 G>A), RS1002050834 (3:196519575 A>G), RS1002083505 (3:196519368 G>A), RS1002092809 (3:196514420 C>A), RS1002170447 (3:196507205 G>A), RS1002245409 (3:196507612 ATT>A), RS1002307969 (3:196515589 G>T), RS1002383761 (3:196521344 T>C), RS1003478490 (3:196509839 T>G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
tebuconazole	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Doxorubicin	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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