SMIM47

Summary

SMIM47 (small integral membrane protein 47, HGNC:53452) is a protein-coding gene on chromosome 19q13.33, encoding Small integral membrane protein 47 (D0EPY3).

Predicted to be located in membrane.

Source: NCBI Gene 105372440 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001384597

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53452
Approved symbol	SMIM47
Name	small integral membrane protein 47
Location	19q13.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000261341
Ensembl biotype	protein_coding
Entrez	105372440

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 nonsense_mediated_decay

ENST00000562076, ENST00000563228, ENST00000636757

RefSeq mRNA: 1 — MANE Select: NM_001384597 NM_001384597

CCDS: CCDS92672

Canonical transcript exons

ENST00000562076 — 3 exons

Exon	Start	End
ENSE00002593766	50786090	50786160
ENSE00002628423	50785942	50786001
ENSE00002629849	50785728	50785823

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 97.54.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	97.54	gold quality
left testis	UBERON:0004533	97.50	gold quality
testis	UBERON:0000473	96.78	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.96	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.60	gold quality
skin of abdomen	UBERON:0001416	65.04	gold quality
zone of skin	UBERON:0000014	63.86	gold quality
skin of leg	UBERON:0001511	62.99	gold quality
adrenal tissue	UBERON:0018303	61.87	gold quality
mucosa of stomach	UBERON:0001199	60.16	gold quality
primary visual cortex	UBERON:0002436	59.27	gold quality
apex of heart	UBERON:0002098	57.32	gold quality
right ovary	UBERON:0002118	57.12	gold quality
granulocyte	CL:0000094	56.45	gold quality
metanephros cortex	UBERON:0010533	55.21	gold quality
lower esophagus mucosa	UBERON:0035834	54.72	gold quality
calcaneal tendon	UBERON:0003701	54.23	gold quality
body of uterus	UBERON:0009853	54.00	gold quality
cerebellum	UBERON:0002037	53.42	gold quality
cerebellar cortex	UBERON:0002129	53.32	gold quality
ovary	UBERON:0000992	53.27	gold quality
prostate gland	UBERON:0002367	53.10	gold quality
cerebellar hemisphere	UBERON:0002245	53.02	gold quality
left ovary	UBERON:0002119	52.71	gold quality
popliteal artery	UBERON:0002250	52.10	gold quality
tibial artery	UBERON:0007610	52.07	gold quality
placenta	UBERON:0001987	51.86	gold quality
left uterine tube	UBERON:0001303	51.82	gold quality
tonsil	UBERON:0002372	51.67	gold quality
body of pancreas	UBERON:0001150	51.53	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	120.04
E-ANND-3	no	2.25

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm15517	ENSMUSG00000087376
rattus_norvegicus	Smim47	ENSRNOG00000084936

Protein

Protein identifiers

Small integral membrane protein 47 — D0EPY3 (reviewed: D0EPY3)

All UniProt accessions (2): D0EPY3, A0A1B0GTG8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001371526* (*=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-D0EPY3-F1	93.53	0.83

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 3 (showing top): NFKBIA_TARGET_GENES, SNRNP70_TARGET_GENES, chr19q13

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: A2CBT5, A5GJ31, A5GQT7, A5GR11, A7M8Z5, A8W3I1, B0JYB0, B1XIN0, B2ITV2, B2Y1W9, B3MFK1, B4HSS0, B4QH87, D0EPY3, O78448, P0A403, P0A404, P12312, P31479, P31590, P51395, P56314, P72701, P72986, Q0ICR0, Q0P3J8, Q0R3M2, Q1RB04, Q1XD92, Q31QD8, Q3AMD6, Q3AUY3, Q5N3U9, Q6B8K0, Q7TUP7, Q7VDM3, Q85AJ9, Q8FGW2, Q8WI22, Q8YNB0

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

755 predictions. Top by Δscore:

Variant	Effect	Δscore
19:50790858:G:GT	donor_gain	1.0000
19:50791797:GA:G	donor_gain	1.0000
19:50791798:A:G	donor_gain	1.0000
19:50792151:G:GT	donor_gain	1.0000
19:50790651:G:GT	donor_gain	0.9900
19:50790698:GGTG:G	donor_loss	0.9900
19:50790699:G:GG	donor_gain	0.9900
19:50790700:T:A	donor_loss	0.9900
19:50790701:GA:G	donor_loss	0.9900
19:50790857:GGAG:G	donor_gain	0.9900
19:50790858:GAGGT:G	donor_loss	0.9900
19:50790859:AGGTA:A	donor_loss	0.9900
19:50790861:GTAG:G	donor_loss	0.9900
19:50790862:T:G	donor_loss	0.9900
19:50791644:ACCCC:A	acceptor_gain	0.9900
19:50791648:C:CA	acceptor_gain	0.9900
19:50791651:TCCA:T	acceptor_loss	0.9900
19:50791652:CCAG:C	acceptor_loss	0.9900
19:50791653:CA:C	acceptor_loss	0.9900
19:50791655:GGT:G	acceptor_gain	0.9900
19:50791741:G:GT	donor_gain	0.9900
19:50791784:GCC:G	donor_gain	0.9900
19:50791785:CCC:C	donor_gain	0.9900
19:50791798:ATAAG:A	donor_loss	0.9900
19:50791799:TAAG:T	donor_loss	0.9900
19:50791800:AAG:A	donor_loss	0.9900
19:50791801:AG:A	donor_loss	0.9900
19:50791802:GG:G	donor_loss	0.9900
19:50791803:G:T	donor_loss	0.9900
19:50791804:T:A	donor_loss	0.9900

AlphaMissense

184 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:50785982:G:T	A20D	0.922
19:50785988:G:T	A18D	0.900
19:50785970:A:T	I24N	0.839
19:50785967:A:C	L25R	0.836
19:50785985:A:C	M19R	0.831
19:50785983:C:G	A20P	0.817
19:50785948:G:C	F31L	0.796
19:50785948:G:T	F31L	0.796
19:50785950:A:G	F31L	0.796
19:50785967:A:G	L25P	0.796
19:50785985:A:T	M19K	0.763
19:50785975:G:C	F22L	0.756
19:50785975:G:T	F22L	0.756
19:50785977:A:G	F22L	0.756
19:50785951:G:C	F30L	0.748
19:50785951:G:T	F30L	0.748
19:50785953:A:G	F30L	0.748
19:50785976:A:G	F22S	0.743
19:50785942:C:A	K33N	0.732
19:50785942:C:G	K33N	0.732
19:50785962:A:G	S27P	0.724
19:50785956:A:C	Y29D	0.704
19:50785967:A:T	L25Q	0.686
19:50785952:A:G	F30S	0.677
19:50786000:T:A	N14I	0.671
19:50785970:A:C	I24S	0.663
19:50785943:T:A	K33M	0.632
19:50785949:A:G	F31S	0.600
19:50785979:A:C	L21W	0.599
19:50785984:C:A	M19I	0.597

dbSNP variants (sampled 300 via entrez): RS1000148259 (19:50787764 C>A,T), RS1000583767 (19:50787531 A>G), RS1001655398 (19:50788104 C>T), RS1003254730 (19:50786966 T>C), RS1004999065 (19:50785905 G>C), RS1005438224 (19:50785758 G>A), RS1006126257 (19:50785463 C>A,T), RS1007127910 (19:50786314 G>A,C), RS1007402655 (19:50787488 C>T), RS1008128796 (19:50787544 CA>C), RS1010822409 (19:50785446 G>A), RS1011833265 (19:50786395 C>T), RS1011864310 (19:50786223 T>C), RS1012282097 (19:50785718 G>A), RS1013210447 (19:50786781 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)

Clinical trials (associated diseases)

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