SMIM24

Summary

SMIM24 (small integral membrane protein 24, HGNC:37244) is a protein-coding gene on chromosome 19p13.3, encoding Small integral membrane protein 24 (O75264).

Predicted to be located in membrane.

Source: NCBI Gene 284422 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 25 total
• MANE Select transcript: NM_001136503

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37244
Approved symbol	SMIM24
Name	small integral membrane protein 24
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	HSPC323
Ensembl gene	ENSG00000095932
Ensembl biotype	protein_coding
Entrez	284422

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000215531, ENST00000586804, ENST00000587847, ENST00000591708

RefSeq mRNA: 1 — MANE Select: NM_001136503 NM_001136503

CCDS: CCDS45915

Canonical transcript exons

ENST00000215531 — 4 exons

Exon	Start	End
ENSE00000655493	3480397	3480525
ENSE00000893040	3478818	3478929
ENSE00003493418	3478419	3478478
ENSE00003722023	3473986	3474996

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 99.77.

FANTOM5 (CAGE): breadth broad, TPM avg 7.0210 / max 1359.1412, expressed in 297 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
178276	2.9364	134
178269	2.3827	61
178272	0.7956	93
178274	0.3420	97
178277	0.3205	47
178273	0.1075	42
178275	0.0537	21
178270	0.0445	16
178271	0.0381	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	99.77	gold quality
ileal mucosa	UBERON:0000331	99.74	gold quality
corpus epididymis	UBERON:0004359	99.67	gold quality
jejunal mucosa	UBERON:0000399	99.42	gold quality
adult mammalian kidney	UBERON:0000082	98.96	gold quality
duodenum	UBERON:0002114	97.48	gold quality
gall bladder	UBERON:0002110	97.33	gold quality
caput epididymis	UBERON:0004358	97.33	gold quality
kidney	UBERON:0002113	96.74	gold quality
adult organism	UBERON:0007023	96.70	gold quality
metanephros cortex	UBERON:0010533	95.15	gold quality
epididymis	UBERON:0001301	94.30	gold quality
cortex of kidney	UBERON:0001225	93.31	gold quality
small intestine Peyer’s patch	UBERON:0003454	93.26	gold quality
small intestine	UBERON:0002108	93.09	gold quality
mucosa of transverse colon	UBERON:0004991	92.79	gold quality
islet of Langerhans	UBERON:0000006	92.23	gold quality
renal medulla	UBERON:0000362	92.20	gold quality
metanephros	UBERON:0000081	91.42	gold quality
bone marrow	UBERON:0002371	88.89	gold quality
rectum	UBERON:0001052	87.88	gold quality
jejunum	UBERON:0002115	86.96	gold quality
sperm	CL:0000019	86.88	gold quality
body of stomach	UBERON:0001161	86.24	gold quality
cauda epididymis	UBERON:0004360	85.97	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.96	gold quality
stomach	UBERON:0000945	85.67	gold quality
bone marrow cell	CL:0002092	84.02	gold quality
thymus	UBERON:0002370	83.75	gold quality
blood	UBERON:0000178	83.73	gold quality

Single-cell (SCXA)

Detected in 27 experiment(s), a significant marker in 23.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	2550.18
E-HCAD-10	yes	1945.62
E-GEOD-124472	yes	1385.73
E-GEOD-114530	yes	1111.95
E-MTAB-9906	yes	1041.70
E-GEOD-81547	yes	563.65
E-CURD-112	yes	458.06
E-ANND-5	yes	440.22
E-MTAB-9067	yes	340.72
E-GEOD-81608	yes	306.55
E-HCAD-6	yes	293.07
E-CURD-55	yes	267.68
E-MTAB-7407	yes	247.39
E-MTAB-8207	yes	134.35
E-HCAD-4	yes	87.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting SMIM24, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-6715B-5P	99.64	69.63	1420
HSA-MIR-4269	99.55	69.89	1373
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-4742-5P	98.89	68.41	1542
HSA-MIR-222-5P	98.75	69.17	1242
HSA-MIR-330-5P	98.73	67.63	1788
HSA-MIR-6837-3P	98.42	66.71	1149
HSA-MIR-4664-5P	98.17	65.07	1020
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-4675	97.69	64.82	774
HSA-MIR-4741	97.69	64.14	883
HSA-MIR-1972	97.67	67.38	1172
HSA-MIR-5187-3P	97.28	67.10	1037

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim24	ENSDARG00000095633
mus_musculus	Smim24	ENSMUSG00000078439
rattus_norvegicus	Smim24	ENSRNOG00000076946

Paralogs (1): PDZK1IP1 (ENSG00000162366)

Protein

Protein identifiers

Small integral membrane protein 24 — O75264 (reviewed: O75264)

All UniProt accessions (2): O75264, K7EKM7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the PDZK1-interacting protein 1/SMIM24 family.

RefSeq proteins (1): NP_001129975* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031627	PDZK1IP1/SMIM24	Family

Pfam: PF15807

UniProt features (8 total): compositionally biased region 2, sequence conflict 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75264-F1	65.61	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 44 (showing top): TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP, chr19p13, NFKBIA_TARGET_GENES, MIR4692, MIR6127, MIR6129, MIR4514, MIR3116, MIR6805_5P, GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2, GAO_LARGE_INTESTINE_24W_C10_ENTEROCYTE, MURARO_PANCREAS_ALPHA_CELL, HAY_BONE_MARROW_CD34_POS_MULTILIN

GO Biological Process (1): biological_process (GO:0008150)

GO Molecular Function (1): molecular_function (GO:0003674)

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

1478 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM24	NYNRIN	Q9P2P1	660
SMIM24	CPXM1	Q96SM3	639
SMIM24	ARHGAP22	Q7Z5H3	623
SMIM24	BEX3	Q00994	575
SMIM24	LAPTM4B	Q86VI4	571
SMIM24	MMRN1	Q13201	508
SMIM24	ZBTB46	Q86UZ6	490
SMIM24	TRAPPC6B	Q86SZ2	486
SMIM24	EMP1	P54849	464
SMIM24	DPYSL3	Q14195	464
SMIM24	ADGRG1	Q9Y653	430
SMIM24	AKR1C3	P42330	421
SMIM24	SOCS2	O14508	371
SMIM24	ZNF583	Q96ND8	369
SMIM24	GUCD1	Q96NT3	364

IntAct

2 interactions, top by confidence:

A	B	Type	Score
MEP1B	SMIM24	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (2): SMIM24 (PCA), RPS6 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GV96, A0MZ66, A0MZ67, A1Z1Q3, A2VDA9, A5PJI6, A6NKN8, A8R4Q8, E7F7X0, O14990, O19021, O42932, O62771, O75167, O75264, P13505, P20810, P27775, P48539, P54866, P63054, P63055, Q04504, Q08DU9, Q148C4, Q15506, Q28IH8, Q3TEA8, Q3UYG8, Q4R615, Q5F3A1, Q5M8L3, Q5R4Q3, Q5SSJ5, Q5U1X0, Q5ZM33, Q62736, Q6GNQ4, Q6NWC9, Q6P3G4

Diamond homologs: O75264, Q0VG18, Q2KIP5, Q13113, Q5RA41, Q6ITQ4, Q6XQ84, Q923S2, Q9CQH0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

25 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	15
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

312 predictions. Top by Δscore:

Variant	Effect	Δscore
19:3474992:CTTCA:C	acceptor_gain	1.0000
19:3474993:TTCA:T	acceptor_gain	1.0000
19:3474994:TCA:T	acceptor_gain	1.0000
19:3474995:CA:C	acceptor_gain	1.0000
19:3474995:CAC:C	acceptor_gain	1.0000
19:3474996:ACTGT:A	acceptor_loss	1.0000
19:3474997:C:CC	acceptor_gain	1.0000
19:3475005:A:AC	acceptor_gain	1.0000
19:3475022:C:CT	acceptor_gain	1.0000
19:3478415:GTACC:G	donor_loss	1.0000
19:3478416:TAC:T	donor_loss	1.0000
19:3478418:C:A	donor_loss	1.0000
19:3478418:CCT:C	donor_gain	1.0000
19:3478474:CAGCC:C	acceptor_gain	1.0000
19:3478475:AGCC:A	acceptor_gain	1.0000
19:3478476:GCC:G	acceptor_gain	1.0000
19:3478477:CC:C	acceptor_gain	1.0000
19:3478477:CCC:C	acceptor_gain	1.0000
19:3478478:CC:C	acceptor_gain	1.0000
19:3478479:C:CA	acceptor_loss	1.0000
19:3478479:C:CC	acceptor_gain	1.0000
19:3478480:T:A	acceptor_loss	1.0000
19:3478813:CCCA:C	donor_loss	1.0000
19:3478814:CCA:C	donor_loss	1.0000
19:3478815:CAC:C	donor_loss	1.0000
19:3478816:ACCT:A	donor_loss	1.0000
19:3478817:C:CT	donor_loss	1.0000
19:3480393:CTA:C	donor_loss	1.0000
19:3480394:TAC:T	donor_loss	1.0000
19:3480395:A:AC	donor_gain	1.0000

AlphaMissense

846 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:3478874:G:C	F41L	0.979
19:3478874:G:T	F41L	0.979
19:3478876:A:G	F41L	0.979
19:3478906:A:G	W31R	0.978
19:3478906:A:T	W31R	0.978
19:3478904:C:A	W31C	0.974
19:3478904:C:G	W31C	0.974
19:3478879:C:G	G40R	0.970
19:3478878:C:T	G40D	0.965
19:3478887:G:T	A37E	0.961
19:3478897:C:G	G34R	0.953
19:3478896:C:T	G34D	0.944
19:3478863:A:T	V45D	0.939
19:3478890:G:T	A36D	0.934
19:3478872:A:C	L42R	0.930
19:3478872:A:T	L42Q	0.929
19:3478875:A:G	F41S	0.911
19:3478872:A:G	L42P	0.907
19:3478881:A:T	V39D	0.902
19:3478866:A:T	I44N	0.901
19:3478854:A:T	V48D	0.898
19:3478893:A:G	L35P	0.892
19:3478845:G:T	A51D	0.891
19:3478888:C:G	A37P	0.889
19:3478861:A:C	Y46D	0.885
19:3478893:A:T	L35Q	0.879
19:3478839:C:G	R53P	0.874
19:3478875:A:C	F41C	0.865
19:3478902:A:G	L32P	0.858
19:3478897:C:A	G34C	0.852

dbSNP variants (sampled 300 via entrez): RS1000173961 (19:3479862 T>A,G), RS1000237971 (19:3482324 G>A,T), RS1000283480 (19:3476907 G>A,T), RS1000287354 (19:3482229 C>T), RS1000440180 (19:3476436 G>A), RS1000690007 (19:3482152 C>A,G,T), RS1001027912 (19:3476763 T>C), RS1001874691 (19:3473548 C>T), RS1002035341 (19:3475063 C>G,T), RS1002445803 (19:3479681 G>A), RS1003295440 (19:3481119 G>A,T), RS1003586716 (19:3479354 G>C), RS1004257385 (19:3475598 G>A,C), RS1004998373 (19:3477826 G>A), RS1005002034 (19:3478259 T>A,C)

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

1 associations (top):

Study	Trait	p-value
GCST90002386_54	High light scatter reticulocyte percentage of red cells	3.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	decreases expression	3
entinostat	increases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	2
Valproic Acid	affects expression, increases expression, increases methylation	2
aristolochic acid I	increases expression	1
methyleugenol	decreases expression	1
propionaldehyde	increases expression	1
bisphenol A	affects expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Zoledronic Acid	decreases expression	1
Leflunomide	decreases expression	1
Carbamazepine	affects expression	1
Diethylhexyl Phthalate	decreases expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Quercetin	decreases expression	1
Silicon Dioxide	decreases expression	1
Urethane	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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