SMIM39

Summary

SMIM39 (small integral membrane protein 39, HGNC:54076) is a protein-coding gene on chromosome 2q21.1, encoding Small integral membrane protein 39 (A0A1B0GW54).

Predicted to be located in membrane.

Source: NCBI Gene 113523639 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001414894

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:54076
Approved symbol	SMIM39
Name	small integral membrane protein 39
Location	2q21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000284479
Ensembl biotype	protein_coding
Entrez	113523639

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000635976, ENST00000710632, ENST00000710633, ENST00000711663

RefSeq mRNA: 1 — MANE Select: NM_001414894 NM_001414894

CCDS: CCDS92867

Canonical transcript exons

ENST00000711663 — 1 exons

Exon	Start	End
ENSE00004016356	131035092	131035262

Expression profiles

Bgee: expression breadth broad, 94 present calls, max score 45.02.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3278 / max 18.3393, expressed in 113 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
22538	0.3278	113

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	45.02	gold quality
apex of heart	UBERON:0002098	42.55	silver quality
skeletal muscle tissue	UBERON:0001134	40.33	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	39.05	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
endocervix	UBERON:0000458	36.82	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
muscle tissue	UBERON:0002385	36.17	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
lymph node	UBERON:0000029	30.89	gold quality
right adrenal gland	UBERON:0001233	30.68	gold quality
prefrontal cortex	UBERON:0000451	30.58	gold quality
gall bladder	UBERON:0002110	30.39	gold quality
right adrenal gland cortex	UBERON:0035827	30.35	gold quality
muscle of leg	UBERON:0001383	30.27	gold quality
right lung	UBERON:0002167	30.20	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
gastrocnemius	UBERON:0001388	29.73	gold quality
ascending aorta	UBERON:0001496	29.41	gold quality
right ovary	UBERON:0002118	29.25	gold quality
myometrium	UBERON:0001296	29.21	gold quality
fundus of stomach	UBERON:0001160	29.07	gold quality
thoracic aorta	UBERON:0001515	29.01	gold quality
blood	UBERON:0000178	28.80	gold quality
duodenum	UBERON:0002114	28.14	gold quality
liver	UBERON:0002107	28.04	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim39	ENSMUSG00000118272

Protein

Protein identifiers

Small integral membrane protein 39 — A0A1B0GW54 (reviewed: A0A1B0GW54)

All UniProt accessions (2): A0A1B0GW54, A0AA34QVT3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001401823* (*=MANE)

Domains & families (InterPro)

UniProt features (2 total): chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GW54-F1	75.68	0.41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr2q21

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GW54, A0A286YFK9, A2BUT1, A2C0D3, A2CCQ3, A5GIA7, A5GM56, A5GQF1, A5GRX8, A5GWF4, A9BDU5, A9BDU7, B7KH61, D5AP83, F7V996, O19930, O40984, O78433, P04123, P0CZ12, P0DTB6, P10306, P17527, P30025, P52587, P55522, P80100, P80259, P89477, P95674, Q00644, Q0IDK0, Q20EW5, Q2JRN5, Q2JRR9, Q2S3T2, Q3AN57, Q3AN59, Q3B0C9, Q7NMA9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

2061 predictions. Top by Δscore:

Variant	Effect	Δscore
2:131038977:G:GA	donor_gain	1.0000
2:131038979:T:TA	donor_gain	1.0000
2:131038980:G:GA	donor_gain	1.0000
2:131040015:GCTGA:G	acceptor_gain	1.0000
2:131040417:C:G	donor_gain	1.0000
2:131040437:GCAT:G	donor_gain	1.0000
2:131040441:G:GG	donor_gain	1.0000
2:131041228:A:AG	acceptor_gain	1.0000
2:131041229:G:GG	acceptor_gain	1.0000
2:131041229:GCAA:G	acceptor_gain	1.0000
2:131041396:TGCAG:T	donor_gain	1.0000
2:131041409:C:T	donor_gain	1.0000
2:131041460:CAGGT:C	donor_loss	1.0000
2:131041461:AGGT:A	donor_loss	1.0000
2:131041462:GGTA:G	donor_loss	1.0000
2:131041463:GT:G	donor_loss	1.0000
2:131041464:T:A	donor_loss	1.0000
2:131041812:CA:C	acceptor_loss	1.0000
2:131041936:G:GT	donor_gain	1.0000
2:131041942:G:GT	donor_gain	1.0000
2:131041942:G:T	donor_gain	1.0000
2:131041943:AGG:A	donor_loss	1.0000
2:131041945:GTG:G	donor_loss	1.0000
2:131044466:G:GT	donor_gain	1.0000
2:131045367:A:AG	acceptor_gain	1.0000
2:131045368:G:GG	acceptor_gain	1.0000
2:131045436:G:T	donor_gain	1.0000
2:131046031:T:TA	acceptor_gain	1.0000
2:131046033:TTCA:T	acceptor_loss	1.0000
2:131046034:TCA:T	acceptor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000173012 (2:131039555 C>T), RS1000267383 (2:131042994 T>A), RS1000317640 (2:131043305 T>A,C), RS1000598248 (2:131044355 G>C,T), RS1000750829 (2:131038199 G>C), RS1000778597 (2:131038186 T>C), RS1000835967 (2:131036633 G>A), RS1001198512 (2:131035004 G>A,C,T), RS1001232084 (2:131037783 C>G), RS1001267941 (2:131038693 C>A), RS1001536249 (2:131037163 G>A,C), RS1001652486 (2:131037467 G>A), RS1001752523 (2:131035554 T>G), RS1001869751 (2:131044888 G>T), RS1001896619 (2:131034483 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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