SNX24

Summary

SNX24 (sorting nexin 24, HGNC:21533) is a protein-coding gene on chromosome 5q23.2, encoding Sorting nexin-24 (Q9Y343). May be involved in several stages of intracellular trafficking.

Predicted to enable phosphatidylinositol phosphate binding activity. Predicted to be involved in protein transport. Predicted to be located in cytoplasmic vesicle membrane.

Source: NCBI Gene 28966 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 32 total
• MANE Select transcript: NM_014035

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21533
Approved symbol	SNX24
Name	sorting nexin 24
Location	5q23.2
Locus type	gene with protein product
Status	Approved
Aliases	SBBI31
Ensembl gene	ENSG00000064652
Ensembl biotype	protein_coding
Entrez	28966

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 7 protein_coding, 6 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000261369, ENST00000395451, ENST00000502387, ENST00000503149, ENST00000506996, ENST00000507364, ENST00000510914, ENST00000511211, ENST00000511545, ENST00000513613, ENST00000513881, ENST00000515729, ENST00000889731, ENST00000916532, ENST00000916533

RefSeq mRNA: 1 — MANE Select: NM_014035 NM_014035

CCDS: CCDS4132

Canonical transcript exons

ENST00000261369 — 7 exons

Exon	Start	End
ENSE00001126281	123007682	123009205
ENSE00002051567	122845613	122845693
ENSE00003550335	122999912	123000006
ENSE00003552582	122936734	122936817
ENSE00003557705	123001405	123001437
ENSE00003614179	123001940	123002004
ENSE00003650258	122946055	122946159

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 96.58.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.0013 / max 157.9496, expressed in 1774 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58222	14.8824	1709
58219	1.5469	981
58218	0.5966	299
58220	0.4667	251
58221	0.3503	161
58217	0.1356	57
58216	0.0227	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	96.58	gold quality
secondary oocyte	CL:0000655	96.29	gold quality
lower esophagus mucosa	UBERON:0035834	95.99	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.94	gold quality
spinal cord	UBERON:0002240	94.09	gold quality
esophagus mucosa	UBERON:0002469	92.51	gold quality
buccal mucosa cell	CL:0002336	92.30	gold quality
esophagus squamous epithelium	UBERON:0006920	91.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.61	gold quality
tibial nerve	UBERON:0001323	91.24	gold quality
epithelium of esophagus	UBERON:0001976	90.20	gold quality
amniotic fluid	UBERON:0000173	89.99	gold quality
corpus callosum	UBERON:0002336	89.21	gold quality
adrenal tissue	UBERON:0018303	89.19	gold quality
esophagus	UBERON:0001043	88.62	gold quality
right lung	UBERON:0002167	88.61	gold quality
substantia nigra	UBERON:0002038	88.45	gold quality
placenta	UBERON:0001987	88.39	gold quality
rectum	UBERON:0001052	88.15	gold quality
midbrain	UBERON:0001891	87.92	gold quality
inferior vagus X ganglion	UBERON:0005363	87.76	gold quality
skin of leg	UBERON:0001511	87.69	gold quality
ascending aorta	UBERON:0001496	87.44	gold quality
left coronary artery	UBERON:0001626	87.44	gold quality
mucosa of stomach	UBERON:0001199	87.43	gold quality
descending thoracic aorta	UBERON:0002345	87.41	gold quality
thoracic aorta	UBERON:0001515	87.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.37	gold quality
upper lobe of left lung	UBERON:0008952	87.06	gold quality
upper lobe of lung	UBERON:0008948	86.95	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting SNX24, 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-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-12129	99.72	67.45	1311
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-18A-3P	99.56	65.68	1092

Literature-anchored findings (GeneRIF, showing 1)

• Sorting nexin 24 is required for alpha-granule biogenesis and cargo delivery in megakaryocytes. (PMID:35021601)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	snx24	ENSDARG00000053527
mus_musculus	Snx24	ENSMUSG00000024535
rattus_norvegicus	Snx24	ENSRNOG00000017488

Paralogs (1): SNX22 (ENSG00000157734)

Protein

Protein identifiers

Sorting nexin-24 — Q9Y343 (reviewed: Q9Y343)

All UniProt accessions (4): Q9Y343, A8MXB7, H0Y8V0, H0YA25

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in several stages of intracellular trafficking.

Subcellular location. Cytoplasmic vesicle membrane.

Domain organisation. The PX domain mediates specific binding to membranes enriched in phosphatidylinositol 3-phosphate (PtdIns(P3)).

Similarity. Belongs to the sorting nexin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y343-1	1	yes
Q9Y343-2	2

RefSeq proteins (1): NP_054754* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001683	PX_dom	Domain
IPR036871	PX_dom_sf	Homologous_superfamily
IPR052467	Sorting_nexin_PX-domain	Family

Pfam: PF00787

UniProt features (17 total): binding site 4, strand 3, helix 3, modified residue 3, chain 1, domain 1, turn 1, splice variant 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
4AZ9	X-RAY DIFFRACTION	1.75
8TBW	X-RAY DIFFRACTION	2.08
8TBV	X-RAY DIFFRACTION	2.64
8U9G	X-RAY DIFFRACTION	2.87

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y343-F1	80.57	0.41

Functional residue map

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

Ligand- & substrate-binding residues (4): 38; 40; 61; 74

Post-translational modifications (3): 1, 113, 116

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 120 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, HEN1_01, VECCHI_GASTRIC_CANCER_EARLY_DN, RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP, SANSOM_APC_TARGETS, SANSOM_APC_TARGETS_REQUIRE_MYC, GOMF_PHOSPHATIDYLINOSITOL_5_PHOSPHATE_BINDING, GOMF_PHOSPHATIDYLINOSITOL_PHOSPHATE_BINDING, GOMF_PHOSPHATIDYLINOSITOL_BINDING, GOMF_PHOSPHATIDYLINOSITOL_3_PHOSPHATE_BINDING, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING, WEST_ADRENOCORTICAL_TUMOR_UP, CHEN_METABOLIC_SYNDROM_NETWORK

GO Biological Process (1): protein transport (GO:0015031)

GO Molecular Function (7): phosphatidylinositol-5-phosphate binding (GO:0010314), phosphatidylinositol-3-phosphate binding (GO:0032266), phosphatidylinositol-4-phosphate binding (GO:0070273), phosphatidylinositol phosphate binding (GO:1901981), protein binding (GO:0005515), lipid binding (GO:0008289), phosphatidylinositol binding (GO:0035091)

GO Cellular Component (3): cytoplasmic vesicle membrane (GO:0030659), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
anion binding	3
phosphatidylinositol phosphate binding	3
binding	2
transport	1
intracellular protein localization	1
establishment of protein localization	1
phospholipid binding	1
vesicle membrane	1
cytoplasmic vesicle	1
cellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

520 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNX24	SNX11	Q9Y5W9	638
SNX24	SNX3	O60493	544
SNX24	SNX10	Q9Y5X0	519
SNX24	SNX20	Q7Z614	515
SNX24	SNX2	P82862	505
SNX24	KIF16B	Q96L93	489
SNX24	SNX21	Q969T3	485
SNX24	SNX16	P57768	478
SNX24	SNX12	Q9UMY4	477
SNX24	LYG1	Q8N1E2	442
SNX24	SNX25	Q9H3E2	427
SNX24	SNX15	Q9NRS6	422
SNX24	ERP27	Q96DN0	411
SNX24	SYTL5	Q8TDW5	394
SNX24	TMEM86A	Q8N2M4	393

IntAct

26 interactions, top by confidence:

A	B	Type	Score
CSNK1A1	FAM83G	psi-mi:“MI:0914”(association)	0.900
CSNK1E	PER2	psi-mi:“MI:0914”(association)	0.850
CSNK1D	PER2	psi-mi:“MI:0914”(association)	0.810
POU2F1	SNX24	psi-mi:“MI:0915”(physical association)	0.560
CSNK1E	ZSWIM8	psi-mi:“MI:0914”(association)	0.530
SPATA46	TYW5	psi-mi:“MI:0914”(association)	0.530
CSNK1E	POTEF	psi-mi:“MI:0914”(association)	0.530
TSSK1B	HSPA8	psi-mi:“MI:0914”(association)	0.530
SPATA46	MDM4	psi-mi:“MI:0914”(association)	0.530
SNX24	Dlg4	psi-mi:“MI:0407”(direct interaction)	0.440
Csnk1e		psi-mi:“MI:0915”(physical association)	0.400
YWHAZ	SNX24	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
CSNK1D	TMEM131L	psi-mi:“MI:0914”(association)	0.350
FGFR2	U2SURP	psi-mi:“MI:0914”(association)	0.350
SNX24	STRN	psi-mi:“MI:0914”(association)	0.350
SNX24	GAPVD1	psi-mi:“MI:0914”(association)	0.350
CSNK1D		psi-mi:“MI:0914”(association)	0.350
POU2F1	SNX24	psi-mi:“MI:0915”(physical association)	0.000
SNX24	SH3GL3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (60): SNX24 (Affinity Capture-MS), SNX24 (Affinity Capture-MS), FLNC (Affinity Capture-MS), KPTN (Affinity Capture-MS), ITFG2 (Affinity Capture-MS), UGP2 (Affinity Capture-MS), RAP1GDS1 (Affinity Capture-MS), SNX24 (Affinity Capture-MS), SNX24 (Affinity Capture-MS), SNX24 (Affinity Capture-MS), SNX24 (Affinity Capture-MS), CSNK1A1 (Affinity Capture-MS), GAPVD1 (Affinity Capture-MS), LONRF2 (Affinity Capture-MS), SNX24 (Affinity Capture-MS)

ESM2 similar proteins: A2AD83, A2CEA7, A5DHC9, A6H8H2, A7TKX9, A8WG21, B7ZC32, F1Q506, F1REV3, F8WLE0, O14827, P10686, P32019, P70392, P97369, P97433, Q05AK5, Q08826, Q09178, Q0IIL5, Q17QS1, Q28HD5, Q3U1T9, Q4FZZ1, Q4QR82, Q5U2S5, Q5VZ89, Q62077, Q6BIS2, Q6CY25, Q6DDY6, Q6FR40, Q6P3S1, Q6P5D3, Q6P8Y7, Q6ZTQ3, Q75R65, Q7Z7A4, Q80UQ2, Q8BX57

Diamond homologs: Q17QS1, Q4G017, Q5U2S5, Q80TM9, Q96L94, Q9CRB0, Q9Y2I1, Q9Y343, Q2T9W1, Q3UR97, Q5BK61, Q7Z614, Q969T3, Q9D2Y5, Q6PHS6, Q9Y5W8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 24 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
protein phosphorylation	5	17.0×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3067 predictions. Top by Δscore:

Variant	Effect	Δscore
5:122845690:CACGG:C	donor_loss	1.0000
5:122845693:GGTA:G	donor_loss	1.0000
5:122845694:GT:G	donor_loss	1.0000
5:122847186:T:G	donor_gain	1.0000
5:122936729:CTCA:C	acceptor_loss	1.0000
5:122936730:TCAGG:T	acceptor_loss	1.0000
5:122936732:A:AG	acceptor_gain	1.0000
5:122936732:A:T	acceptor_loss	1.0000
5:122936733:G:GG	acceptor_gain	1.0000
5:122936733:GGT:G	acceptor_gain	1.0000
5:122936814:AAAGG:A	donor_loss	1.0000
5:122936815:AAGG:A	donor_loss	1.0000
5:122936816:AGG:A	donor_loss	1.0000
5:122936817:GGTAA:G	donor_loss	1.0000
5:122936818:G:A	donor_loss	1.0000
5:122936819:T:G	donor_loss	1.0000
5:122946156:ACAGG:A	donor_loss	1.0000
5:122946158:AGG:A	donor_loss	1.0000
5:122946159:GGTA:G	donor_loss	1.0000
5:122946161:T:G	donor_loss	1.0000
5:123024000:CTGT:C	acceptor_gain	1.0000
5:123024004:C:CC	acceptor_gain	1.0000
5:123025779:TTTA:T	donor_loss	1.0000
5:123025780:TTA:T	donor_loss	1.0000
5:123025781:TACCA:T	donor_loss	1.0000
5:123025782:A:AT	donor_loss	1.0000
5:123025782:ACCAT:A	donor_gain	1.0000
5:123025783:C:CG	donor_loss	1.0000
5:123025783:CCAT:C	donor_gain	1.0000
5:123025783:CCATC:C	donor_gain	1.0000

AlphaMissense

1103 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:122936737:T:C	F22L	1.000
5:122936738:T:C	F22S	1.000
5:122936739:T:A	F22L	1.000
5:122936739:T:G	F22L	1.000
5:122936785:A:G	R38G	1.000
5:122936786:G:C	R38T	1.000
5:122936786:G:T	R38I	1.000
5:122936787:A:C	R38S	1.000
5:122936787:A:T	R38S	1.000
5:122936788:T:C	Y39H	1.000
5:122936788:T:G	Y39D	1.000
5:122936789:A:G	Y39C	1.000
5:122936798:T:C	F42S	1.000
5:122946056:T:C	L49P	1.000
5:122946086:C:A	P59H	1.000
5:122946091:A:G	K61E	1.000
5:122946092:A:T	K61I	1.000
5:122946093:A:C	K61N	1.000
5:122946093:A:T	K61N	1.000
5:122946098:T:A	V63D	1.000
5:122946102:G:C	R64S	1.000
5:122946102:G:T	R64S	1.000
5:122946131:G:C	R74P	1.000
5:122946134:G:C	R75P	1.000
5:122946143:T:C	L78S	1.000
5:122946151:T:G	Y81D	1.000
5:122999957:T:C	F99L	1.000
5:122999958:T:C	F99S	1.000
5:122999959:C:A	F99L	1.000
5:122999959:C:G	F99L	1.000

dbSNP variants (sampled 300 via entrez): RS1000000360 (5:122858334 G>A,T), RS1000017676 (5:122916522 C>T), RS1000025420 (5:122851480 T>A), RS1000036843 (5:122851282 A>C), RS1000039200 (5:122973788 C>T), RS1000046130 (5:122891661 T>G), RS1000066174 (5:122979360 C>G), RS1000069248 (5:123020606 A>T), RS1000072871 (5:122938430 T>G), RS1000114069 (5:122883171 A>G), RS1000115874 (5:122965100 A>G), RS1000127782 (5:122881801 T>C), RS1000159655 (5:122921713 G>A,C), RS1000180552 (5:122881572 A>T), RS1000190131 (5:122956068 T>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

7 associations (top):

Study	Trait	p-value
GCST002726_22	Glucose homeostasis traits	8.000000e-06
GCST004607_237	Plateletcrit	2.000000e-13
GCST010242_186	HDL cholesterol levels	5.000000e-08
GCST010701_69	Cortical surface area (MOSTest)	2.000000e-09
GCST010702_176	Subcortical volume (MOSTest)	8.000000e-35
GCST010703_344	Brain morphology (MOSTest)	4.000000e-10
GCST90002395_457	Mean platelet volume	4.000000e-28

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0006831	acute insulin response measurement
EFO:0007985	platelet crit
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	6
trichostatin A	affects cotreatment, increases expression	3
sodium arsenite	decreases expression, increases abundance, increases expression	3
Benzo(a)pyrene	decreases methylation, decreases expression	3
arsenite	affects binding, increases reaction, increases methylation	2
Vorinostat	increases expression, affects cotreatment	2
Estradiol	affects binding, increases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
cinnamaldehyde	increases expression	1
mono-(2-ethylhexyl)phthalate	decreases methylation, increases abundance	1
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
hydroquinone	increases expression	1
diallyl trisulfide	increases expression	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
K 7174	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
jinfukang	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	decreases expression, increases abundance	1
Cisplatin	affects cotreatment, decreases expression	1
Coumestrol	affects cotreatment, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Diethylhexyl Phthalate	decreases methylation, increases abundance	1

Clinical trials (associated diseases)

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