SMIM41

Summary

SMIM41 (small integral membrane protein 41, HGNC:54075) is a protein-coding gene on chromosome 12q13.13, encoding Small integral membrane protein 41 (A0A2R8YCJ5).

Predicted to be located in membrane.

Source: NCBI Gene 113523638 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001369216

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:54075
Approved symbol	SMIM41
Name	small integral membrane protein 41
Location	12q13.13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000284791
Ensembl biotype	protein_coding
Entrez	113523638

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000546390

RefSeq mRNA: 1 — MANE Select: NM_001369216 NM_001369216

CCDS: CCDS91699

Canonical transcript exons

ENST00000546390 — 3 exons

Exon	Start	End
ENSE00002335755	52079704	52080181
ENSE00002377537	52083894	52083968
ENSE00002379002	52107379	52108255

Expression profiles

Bgee: expression breadth broad, 96 present calls, max score 84.59.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7013 / max 104.3717, expressed in 161 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125574	0.4895	103
206707	0.1770	44
125572	0.0188	10
125573	0.0162	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lung	UBERON:0002167	84.59	gold quality
sural nerve	UBERON:0015488	81.54	gold quality
upper lobe of left lung	UBERON:0008952	79.73	gold quality
tibial nerve	UBERON:0001323	76.74	gold quality
lung	UBERON:0002048	74.52	gold quality
spleen	UBERON:0002106	67.45	gold quality
prostate gland	UBERON:0002367	66.67	gold quality
left ovary	UBERON:0002119	64.42	gold quality
mucosa of transverse colon	UBERON:0004991	64.17	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	63.82	gold quality
ovary	UBERON:0000992	63.42	gold quality
lower esophagus muscularis layer	UBERON:0035833	62.35	gold quality
right atrium auricular region	UBERON:0006631	62.29	gold quality
lower esophagus	UBERON:0013473	62.25	gold quality
right ovary	UBERON:0002118	61.90	gold quality
right testis	UBERON:0004534	61.40	gold quality
urinary bladder	UBERON:0001255	60.72	gold quality
left testis	UBERON:0004533	60.71	gold quality
testis	UBERON:0000473	60.33	gold quality
body of stomach	UBERON:0001161	59.31	gold quality
esophagus	UBERON:0001043	58.20	gold quality
apex of heart	UBERON:0002098	58.01	gold quality
fundus of stomach	UBERON:0001160	57.86	gold quality
stomach	UBERON:0000945	57.32	gold quality
gall bladder	UBERON:0002110	56.65	gold quality
lower esophagus mucosa	UBERON:0035834	55.65	gold quality
esophagus mucosa	UBERON:0002469	55.61	gold quality
small intestine Peyer’s patch	UBERON:0003454	55.47	gold quality
rectum	UBERON:0001052	55.15	gold quality
calcaneal tendon	UBERON:0003701	54.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.06

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Small integral membrane protein 41 — A0A2R8YCJ5 (reviewed: A0A2R8YCJ5)

All UniProt accessions (1): A0A2R8YCJ5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001356145* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR043383	Reprimo_fam	Family

UniProt features (4 total): chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A2R8YCJ5-F1	74.73	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr12q13

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

136 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM41	SMIM31	A0A1B0GVY4	713
SMIM41	SMIM36	A0A1B0GVT2	678
SMIM41	SMIM38	A0A286YFK9	664
SMIM41	C1orf232	A0A0U1RR37	662
SMIM41	EDDM13	A0A1B0GTR0	662
SMIM41	TMDD1	P0DPE3	654
SMIM41	SCYGR7	A0A286YF01	651
SMIM41	FAM240C	A0A1B0GVR7	623
SMIM41	C10orf143	A0A1B0GUT2	598
SMIM41	CCDC201	A0A1B0GTI1	585
SMIM41	SMIM28	A0A1B0GU29	580
SMIM41	ETDA	Q3ZM63	542
SMIM41	ETDC	A0A1B0GVM5	542
SMIM41	SCYGR1	A0A286YEY9	506
SMIM41	BTBD8	Q5XKL5	370

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A2R8YCJ5, A2A699, A2AEV7, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NL88, A8MVW0, A9JSM3, B2RU40, B8ZZ34, C9JH25, D4A9R4, J3QNX5, P0CG09, P98077, Q0VD38, Q14761, Q17QH7, Q29RK8, Q2KJ18, Q2M3V2, Q3SX20, Q5BJT1, Q5HZJ5, Q5RKR3, Q5T442, Q64697, Q69YZ2, Q6PB97, Q6PCT2, Q6UXK2, Q6ZMQ8, Q6ZVH7, Q6ZW31, Q80XF7, Q8BLS7

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

576 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:52079927:G:A	G50R	0.982
12:52079927:G:C	G50R	0.982
12:52079928:G:A	G50E	0.979
12:52079924:T:C	C49R	0.972
12:52079942:G:C	G55R	0.970
12:52079943:G:A	G55D	0.963
12:52079900:G:C	G41R	0.958
12:52079913:T:G	L45R	0.957
12:52079931:T:A	V51D	0.947
12:52079922:T:A	L48H	0.945
12:52079919:T:A	V47E	0.938
12:52079936:T:C	F53L	0.938
12:52079938:C:A	F53L	0.938
12:52079938:C:G	F53L	0.938
12:52079916:T:G	L46R	0.937
12:52079901:G:A	G41D	0.934
12:52079922:T:G	L48R	0.934
12:52079907:T:G	L43R	0.930
12:52079934:T:G	L52R	0.920
12:52079927:G:T	G50W	0.914
12:52079952:T:A	L58H	0.907
12:52079913:T:A	L45Q	0.904
12:52079952:T:C	L58P	0.901
12:52079907:T:A	L43Q	0.897
12:52079937:T:C	F53S	0.896
12:52079904:T:A	V42E	0.883
12:52079907:T:C	L43P	0.874
12:52079945:G:C	G56R	0.869
12:52079934:T:A	L52Q	0.868
12:52079913:T:C	L45P	0.861

dbSNP variants (sampled 300 via entrez): RS1000047042 (12:52086991 G>C), RS1000101739 (12:52083672 G>A), RS1000401001 (12:52087702 C>T), RS1000424604 (12:52094901 C>A), RS1000524517 (12:52080781 G>A,C), RS1000643033 (12:52088104 T>G), RS1001017165 (12:52097379 AG>A), RS1001133763 (12:52086643 C>T), RS1001263630 (12:52090428 G>T), RS1001392860 (12:52097678 G>A,C), RS1001683708 (12:52093198 A>G), RS1001737527 (12:52093009 G>A,C), RS1001923702 (12:52085872 C>G), RS1001986827 (12:52087330 G>A,C), RS1002173601 (12:52078838 A>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)

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression	1
Smoke	increases abundance, increases expression	1

Clinical trials (associated diseases)

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