SMIM45

Summary

SMIM45 (small integral membrane protein 45, HGNC:27930) is a protein-coding gene on chromosome 22q13.2, encoding Small integral membrane protein 45 (A0A590UK83). Plays a role in the regulation of neuron maturation.

Involved in neuron maturation. Located in cytoplasm and nucleus.

Source: NCBI Gene 339674 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• MANE Select transcript: NM_001395940

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27930
Approved symbol	SMIM45
Name	small integral membrane protein 45
Location	22q13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205704
Ensembl biotype	protein_coding
Entrez	339674

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000381348, ENST00000711329, ENST00000884376, ENST00000884377, ENST00000884378, ENST00000884379, ENST00000884380, ENST00000945271, ENST00000945272, ENST00000945273, ENST00000945274

RefSeq mRNA: 13 — MANE Select: NM_001395940 NM_001395940, NM_001395941, NM_001395942, NM_001395943, NM_001395944, NM_001395945, NM_001395946, NM_001395947, NM_001395948, NM_001395949, NM_001395950, NM_001395951, NM_001395952

CCDS: CCDS93175

Canonical transcript exons

ENST00000381348 — 2 exons

Exon	Start	End
ENSE00002224188	41957672	41958939
ENSE00002245296	41952150	41952421

Expression profiles

Bgee: expression breadth broad, 96 present calls, max score 93.06.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.9159 / max 54.2742, expressed in 101 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
192522	0.7569	100
192523	0.1589	69

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	93.06	gold quality
nucleus accumbens	UBERON:0001882	92.10	gold quality
putamen	UBERON:0001874	91.98	gold quality
prefrontal cortex	UBERON:0000451	91.46	gold quality
quadriceps femoris	UBERON:0001377	91.39	gold quality
caudate nucleus	UBERON:0001873	91.25	gold quality
Ammon’s horn	UBERON:0001954	90.64	gold quality
temporal lobe	UBERON:0001871	90.50	gold quality
amygdala	UBERON:0001876	90.46	gold quality
frontal cortex	UBERON:0001870	90.34	gold quality
anterior cingulate cortex	UBERON:0009835	89.63	gold quality
cerebral cortex	UBERON:0000956	89.55	gold quality
superior frontal gyrus	UBERON:0002661	89.30	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	89.00	gold quality
right frontal lobe	UBERON:0002810	88.93	gold quality
Brodmann (1909) area 9	UBERON:0013540	88.64	gold quality
primary visual cortex	UBERON:0002436	88.29	gold quality
hypothalamus	UBERON:0001898	86.50	gold quality
brain	UBERON:0000955	85.50	gold quality
substantia nigra	UBERON:0002038	84.13	gold quality
thymus	UBERON:0002370	82.33	silver quality
spinal cord	UBERON:0002240	78.49	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.48	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.22	gold quality
cerebellum	UBERON:0002037	76.83	gold quality
cerebellar cortex	UBERON:0002129	76.76	gold quality
cerebellar hemisphere	UBERON:0002245	76.68	gold quality
cortical plate	UBERON:0005343	74.95	gold quality
ventricular zone	UBERON:0003053	73.40	gold quality
ganglionic eminence	UBERON:0004023	69.20	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.80

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Long Noncoding RNA LINC00634 Functions as an Oncogene in Esophageal Squamous Cell Carcinoma Through the miR-342-3p/Bcl2L1 Axis. (PMID:32583748)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim45	ENSMUSG00000068099
rattus_norvegicus	Smim45	ENSRNOG00000043197

Protein

Protein identifiers

Small integral membrane protein 45 — A0A590UK83 (reviewed: A0A590UK83)

All UniProt accessions (1): A0A590UK83

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the regulation of neuron maturation.

Subcellular location. Nucleus. Cytoplasm. Membrane.

Tissue specificity. Highly expressed in brain.

RefSeq proteins (13): NP_001382869, NP_001382870, NP_001382871, NP_001382872, NP_001382873, NP_001382874, NP_001382875, NP_001382876, NP_001382877, NP_001382878, NP_001382879, NP_001382880, NP_001382881 (=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-A0A590UK83-F1	72.71	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 13 (showing top): GOBP_NEURON_MATURATION, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_NEUROGENESIS, GOBP_ANATOMICAL_STRUCTURE_MATURATION, GOBP_CELL_MATURATION, chr22q13, NFKBIA_TARGET_GENES, ZNF322_TARGET_GENES, GOBP_DEVELOPMENTAL_MATURATION, DESCARTES_MAIN_FETAL_SYMPATHOBLASTS, DESCARTES_FETAL_ADRENAL_SYMPATHOBLASTS, GOBP_GENERATION_OF_NEURONS, GOBP_NEURON_DEVELOPMENT

GO Biological Process (2): neuron maturation (GO:0042551), nervous system development (GO:0007399)

GO Molecular Function (0):

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cell maturation	1
neuron development	1
system development	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GRQ0, A0A1B0GSZ0, A0A1B0GVT2, A0A590UK83, A0PK05, A2VDU1, A2VE22, A4QNL6, A5D7B5, A5D992, O43609, O75324, P0DKX4, P29414, P61807, P61808, Q0VFM5, Q15053, Q16655, Q17Q87, Q1L0X2, Q2KIK3, Q2TBG9, Q3MHM8, Q498C7, Q4V921, Q58CU5, Q5RBD8, Q5RF07, Q5RGQ8, Q64448, Q6UWT2, Q80ZU4, Q8BGN6, Q8BUM6, Q8C3K5, Q8C817, Q8K1D8, Q8N6S5, Q91VT8

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

438 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000008935 (22:41954293 G>A,T), RS1000123218 (22:41954547 G>T), RS1000256694 (22:41948269 A>C), RS1000280347 (22:41955511 C>A), RS1000332351 (22:41955370 G>A), RS1000469072 (22:41957954 G>C,T), RS1000600527 (22:41949357 AT>A), RS1000613506 (22:41959427 T>G), RS1000912935 (22:41949566 G>C), RS1001004621 (22:41952730 C>T), RS1001118911 (22:41953084 A>G), RS1001283192 (22:41954065 T>G), RS1001362814 (22:41955238 T>C), RS1001378232 (22:41947167 C>A,T), RS1001468470 (22:41948959 G>A)

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

5 associations (top):

Study	Trait	p-value
GCST004364_23	Intelligence	3.000000e-10
GCST004364_5	Intelligence	3.000000e-10
GCST004521_244	Autism spectrum disorder or schizophrenia	4.000000e-09
GCST006803_13	Schizophrenia	2.000000e-14
GCST007600_34	Alzheimer’s disease	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs8140869	CENPM, SMIM45		0.00	0

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
pentanal	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Niclosamide	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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