SMIM31

Summary

SMIM31 (small integral membrane protein 31, HGNC:49638) is a protein-coding gene on chromosome 4q32.3, encoding Small integral membrane protein 31 (A0A1B0GVY4).

Predicted to be located in membrane.

Source: NCBI Gene 100505989 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001352885

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:49638
Approved symbol	SMIM31
Name	small integral membrane protein 31
Location	4q32.3
Locus type	gene with protein product
Status	Approved
Aliases	h.EPR
Ensembl gene	ENSG00000248771
Ensembl biotype	protein_coding
Entrez	100505989

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000507311, ENST00000515485

RefSeq mRNA: 1 — MANE Select: NM_001352885 NM_001352885

CCDS: CCDS87279

Canonical transcript exons

ENST00000507311 — 3 exons

Exon	Start	End
ENSE00002021531	164754131	164754411
ENSE00002034932	164801091	164803795
ENSE00003822965	164770419	164770555

Expression profiles

Bgee: expression breadth broad, 84 present calls, max score 96.32.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2531 / max 67.7241, expressed in 39 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
50412	0.0793	22
50410	0.0692	22
50411	0.0355	17
50417	0.0162	7
50415	0.0151	7
50416	0.0118	7
50413	0.0093	5
50409	0.0084	4
50414	0.0084	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	96.32	gold quality
jejunal mucosa	UBERON:0000399	94.70	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.34	gold quality
colonic mucosa	UBERON:0000317	93.18	gold quality
ileal mucosa	UBERON:0000331	92.78	gold quality
duodenum	UBERON:0002114	88.09	gold quality
rectum	UBERON:0001052	86.54	gold quality
nasal cavity epithelium	UBERON:0005384	85.94	gold quality
bronchial epithelial cell	CL:0002328	84.06	gold quality
bronchus	UBERON:0002185	83.50	gold quality
buccal mucosa cell	CL:0002336	78.87	gold quality
mucosa of transverse colon	UBERON:0004991	78.23	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.07	gold quality
gall bladder	UBERON:0002110	77.02	gold quality
jejunum	UBERON:0002115	76.69	gold quality
nasal cavity mucosa	UBERON:0001826	76.46	gold quality
small intestine	UBERON:0002108	74.49	gold quality
small intestine Peyer’s patch	UBERON:0003454	73.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.93	silver quality
mucosa of paranasal sinus	UBERON:0005030	72.87	gold quality
epithelial cell of pancreas	CL:0000083	71.40	silver quality
transverse colon	UBERON:0001157	70.93	gold quality
palpebral conjunctiva	UBERON:0001812	68.78	gold quality
colonic epithelium	UBERON:0000397	67.90	gold quality
prostate gland	UBERON:0002367	67.66	gold quality
tibia	UBERON:0000979	67.04	gold quality
intestine	UBERON:0000160	66.89	gold quality
islet of Langerhans	UBERON:0000006	66.09	gold quality
large intestine	UBERON:0000059	64.12	gold quality
trachea	UBERON:0003126	63.37	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-86618	yes	108.35
E-CURD-114	yes	45.08
E-ANND-3	yes	5.05

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 4)

• LINC01207 was highly expressed in pancreatic cancer. Functionally, LINC01207 can bind to miR-143. Its silencing down-regulated the expression of AGR2 by up-regulating miR-143. Moreover, silencing of LINC01207 and up-regulation of miR-143-5p promoted cell apoptosis and autophagy, corresponding to increased expression of autophagy- and apoptosis-related proteins, in addition to inhibited cell growth. (PMID:30991076)
• LINC01207 Predicts Poor Prognosis and Suppresses Cell Growth and Metastasis via Regulating GSK-3beta/beta-Catenin Signaling Pathway in Malignant Glioma. (PMID:32533688)
• CTCF-induced upregulation of LINC01207 promotes gastric cancer progression via miR-1301-3p/PODXL axis. (PMID:33495099)
• Long non-coding RNA LINC01207 promotes cell proliferation and migration but suppresses apoptosis and autophagy in oral squamous cell carcinoma by the microRNA-1301-3p/lactate dehydrogenase isoform A axis. (PMID:34463208)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim31	ENSMUSG00000074300
rattus_norvegicus	Smim31	ENSRNOG00000057966

Protein

Protein identifiers

Small integral membrane protein 31 — A0A1B0GVY4 (reviewed: A0A1B0GVY4)

All UniProt accessions (1): A0A1B0GVY4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001339814* (*=MANE)

Domains & families (InterPro)

UniProt features (7 total): compositionally biased region 2, chain 1, transmembrane region 1, region of interest 1, glycosylation site 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GVY4-F1	66.26	0.22

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 58

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): chr4q32, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN, RATTENBACHER_BOUND_BY_CELF1, GSE14415_INDUCED_TREG_VS_TCONV_DN, GSE13547_WT_VS_ZFX_KO_BCELL_ANTI_IGM_STIM_12H_DN, BARX1_TARGET_GENES, CREB3L4_TARGET_GENES, DLX2_TARGET_GENES, DLX4_TARGET_GENES, E2F2_TARGET_GENES, TEAD2_TARGET_GENES, ZNF407_TARGET_GENES, TOX4_TARGET_GENES, DNMT1_TARGET_GENES

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

138 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM31	SMIM41	A0A2R8YCJ5	713
SMIM31	GOLGA8M	H3BSY2	665
SMIM31	CCDC201	A0A1B0GTI1	630
SMIM31	C10orf143	A0A1B0GUT2	621
SMIM31	LRRC9	Q6ZRR7	611
SMIM31	SMIM36	A0A1B0GVT2	497
SMIM31	SMIM38	A0A286YFK9	480
SMIM31	EDDM13	A0A1B0GTR0	479
SMIM31	C1orf232	A0A0U1RR37	478
SMIM31	TMDD1	P0DPE3	474
SMIM31	SCYGR7	A0A286YF01	473
SMIM31	GARIN4	Q8IYT1	471
SMIM31	FAM240C	A0A1B0GVR7	447
SMIM31	KPRP	Q5T749	401
SMIM31	SMIM28	A0A1B0GU29	380

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GVY4, A4GBX8, A4GCK9, A4K144, A4U7A7, P03491, P05778, P0DOF5, P0DOF8, P10920, P10921, P21430, P26129, P35938, P63232, P67866, P67867, Q04261, Q05637, Q0A2D6, Q0A2I6, Q0HD59, Q20NW0, Q2PIK5, Q2PIM1, Q2PIM5, Q30NQ0, Q38SQ7, Q3V2G4, Q3YPZ4, Q463X4, Q67160, Q67168, Q67176, Q67179, Q6XT33, Q6XT43, Q6XTV0, Q76R36, Q76V04

Diamond homologs: A0A1B0GVY4, Q3V2G4

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

470 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:164770477:T:C	F12L	0.981
4:164770479:C:A	F12L	0.981
4:164770479:C:G	F12L	0.981
4:164770470:A:C	E9D	0.980
4:164770470:A:T	E9D	0.980
4:164770492:T:C	F17L	0.972
4:164770494:T:A	F17L	0.972
4:164770494:T:G	F17L	0.972
4:164770490:C:A	A16D	0.966
4:164770460:C:T	T6I	0.960
4:164770520:C:A	A26D	0.960
4:164770469:A:T	E9V	0.958
4:164770468:G:A	E9K	0.953
4:164770522:T:C	S27P	0.949
4:164770481:T:A	I13N	0.943
4:164770517:T:C	L25P	0.942
4:164770510:T:C	F23L	0.941
4:164770512:T:A	F23L	0.941
4:164770512:T:G	F23L	0.941
4:164770501:T:C	F20L	0.940
4:164770503:T:A	F20L	0.940
4:164770503:T:G	F20L	0.940
4:164770496:T:A	V18D	0.934
4:164770469:A:G	E9G	0.931
4:164770481:T:C	I13T	0.930
4:164770475:C:A	A11E	0.923
4:164770466:T:C	L8S	0.921
4:164770511:T:C	F23S	0.921
4:164770478:T:C	F12S	0.919
4:164770489:G:C	A16P	0.916

dbSNP variants (sampled 300 via entrez): RS10000366 (4:164766106 G>C), RS1000078670 (4:164793290 T>C), RS1000165520 (4:164794631 C>G), RS1000213573 (4:164775856 C>T), RS10002510 (4:164763148 T>C), RS10002762 (4:164772555 C>G,T), RS10003015 (4:164772672 G>A,C), RS1000309940 (4:164769754 A>C), RS10003292 (4:164767119 C>T), RS1000342041 (4:164770010 C>A,T), RS1000358156 (4:164776545 C>T), RS10003667 (4:164767310 G>A,C,T), RS1000366747 (4:164794409 A>G), RS1000393642 (4:164799707 G>C), RS1000454554 (4:164788641 C>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation	1
aflatoxin B2	decreases methylation	1
(+)-JQ1 compound	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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