SMIM40

Summary

SMIM40 (small integral membrane protein 40, HGNC:54073) is a protein-coding gene on chromosome 6p21.32, encoding Small integral membrane protein 40 (Q5STR5).

Predicted to be located in membrane. Predicted to be active in nucleus.

Source: NCBI Gene 113523636 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001369203

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:54073
Approved symbol	SMIM40
Name	small integral membrane protein 40
Location	6p21.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000286920
Ensembl biotype	protein_coding
Entrez	113523636

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000494082

RefSeq mRNA: 1 — MANE Select: NM_001369203 NM_001369203

CCDS: CCDS93891

Canonical transcript exons

ENST00000414388 — 0 exons

Expression profiles

Bgee: expression breadth broad, 12 present calls, max score 57.04.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0221 / max 20.5757, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
73156	0.0221	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	57.04	gold quality
bone marrow cell	CL:0002092	39.15	gold quality
lymph node	UBERON:0000029	38.04	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
primary visual cortex	UBERON:0002436	32.45	silver quality
rectum	UBERON:0001052	32.16	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
left testis	UBERON:0004533	30.43	silver quality
testis	UBERON:0000473	30.41	silver quality
right testis	UBERON:0004534	30.15	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
tonsil	UBERON:0002372	28.89	gold quality
urinary bladder	UBERON:0001255	28.57	gold quality
duodenum	UBERON:0002114	28.14	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	27.89	silver quality
cerebellum	UBERON:0002037	27.29	gold quality
cerebellar cortex	UBERON:0002129	27.20	gold quality
islet of Langerhans	UBERON:0000006	27.06	silver quality
cerebellar hemisphere	UBERON:0002245	26.94	gold quality
pancreas	UBERON:0001264	26.70	silver quality
monocyte	CL:0000576	26.59	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
placenta	UBERON:0001987	25.81	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	40.09

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim40	ENSMUSG00000092349
mus_musculus	Smim40-ps	ENSMUSG00000115113
rattus_norvegicus	Smim40	ENSRNOG00000087561

Protein

Protein identifiers

Small integral membrane protein 40 — Q5STR5 (reviewed: Q5STR5)

All UniProt accessions (1): Q5STR5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001356132* (*=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-Q5STR5-F1	76.77	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 10 (showing top): IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR, WP_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS, WP_MAPK_SIGNALING, WP_P38_MAPK_SIGNALING, WP_APOPTOSIS_MODULATION_AND_SIGNALING, WP_FAS_LIGAND_PATHWAY_AND_STRESS_INDUCTION_OF_HEAT_SHOCK_PROTEINS, WP_ANDROGEN_RECEPTOR_SIGNALING, WP_NUCLEOSOME_REMODELING_COMPLEX, WP_TESSADORIBICKNELLVAN_HAAFTEN_SYNDROME_VARIANTS_NUCLEOSOME_ASSEMBLY, chr6p21

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

6 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM40	CXorf66	Q5JRM2	287
SMIM40	CATSPERE	Q5SY80	176
SMIM40	RPSA	P08865	166

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTQ4, A0A286YFK9, A0A291NUG3, A3PNA8, A4WCS4, A4WNL6, A6TBY2, A7HIY9, A8LMA3, B1VPE7, B4TBK3, B4UKG2, B5BCL0, B5EZL8, B5FPH7, B5R317, B5RCG1, B5XNU5, B8JDK6, B8XX90, B9KNZ3, C6DA53, O54625, P0C737, P0C738, P0C739, P0DJZ4, P0DJZ5, P0DQW1, P10306, P62816, P62817, Q00336, Q00644, Q16A98, Q1GXL5, Q28487, Q2IHR6, Q2Q5T5, Q2RP13

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

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000053254 (6:33329538 C>G), RS1000079511 (6:33329495 T>G), RS1000111864 (6:33330121 A>T), RS1000431501 (6:33329831 G>C), RS1001032126 (6:33331096 C>T), RS1001232931 (6:33329075 C>G), RS1001484248 (6:33330756 A>T), RS1001790476 (6:33328588 A>G), RS1002049894 (6:33323287 G>A,C,T), RS1002186003 (6:33323136 C>G), RS1002308293 (6:33327881 G>A,C,T), RS1002338110 (6:33325683 T>A), RS1002390356 (6:33329366 A>C), RS1002393392 (6:33330185 C>T), RS1003238652 (6:33324914 GA>G,GAA,GAAAAAAAAA,GAAAAAAAAAA,GAAAAAAAAAAAAA,GAAAAAAAAAAAAAAA,GAAAAAAAAAAAAAAAA,GAAAAAAAAAAAAAAAAAAA)

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.