SNX30

Summary

SNX30 (sorting nexin family member 30, HGNC:23685) is a protein-coding gene on chromosome 9q32, encoding Sorting nexin-30 (Q5VWJ9). Involved in the regulation of endocytosis and in several stages of intracellular trafficking.

Predicted to enable phosphatidylinositol binding activity. Involved in positive regulation of autophagosome assembly and protein transport. Is active in early endosome.

Source: NCBI Gene 401548 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 75 total — 1 pathogenic
• MANE Select transcript: NM_001012994

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23685
Approved symbol	SNX30
Name	sorting nexin family member 30
Location	9q32
Locus type	gene with protein product
Status	Approved
Aliases	ATG24A
Ensembl gene	ENSG00000148158
Ensembl biotype	protein_coding
OMIM	620955
Entrez	401548

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000374232, ENST00000416585, ENST00000604751, ENST00000870319

RefSeq mRNA: 1 — MANE Select: NM_001012994 NM_001012994

CCDS: CCDS43865

Canonical transcript exons

ENST00000374232 — 9 exons

Exon	Start	End
ENSE00001317626	112838498	112838697
ENSE00001382066	112850859	112850945
ENSE00001462854	112868784	112874987
ENSE00001462855	112750760	112751157
ENSE00001646372	112830725	112830883
ENSE00001674782	112817705	112817815
ENSE00001772008	112836214	112836409
ENSE00001794004	112804776	112804967
ENSE00003587549	112864247	112864399

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 93.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.4585 / max 252.8718, expressed in 1724 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98059	10.4585	1724

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	93.34	gold quality
lower lobe of lung	UBERON:0008949	90.04	gold quality
ileal mucosa	UBERON:0000331	89.86	gold quality
corpus callosum	UBERON:0002336	89.78	gold quality
monocyte	CL:0000576	88.93	gold quality
jejunal mucosa	UBERON:0000399	88.65	gold quality
inferior vagus X ganglion	UBERON:0005363	88.52	gold quality
leukocyte	CL:0000738	88.47	gold quality
cerebellar vermis	UBERON:0004720	88.30	gold quality
subthalamic nucleus	UBERON:0001906	87.02	gold quality
medial globus pallidus	UBERON:0002477	86.95	gold quality
Brodmann (1909) area 46	UBERON:0006483	86.68	gold quality
globus pallidus	UBERON:0001875	86.42	gold quality
lung	UBERON:0002048	86.17	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.27	gold quality
middle temporal gyrus	UBERON:0002771	85.18	gold quality
secondary oocyte	CL:0000655	85.06	gold quality
spinal cord	UBERON:0002240	85.01	gold quality
dorsal plus ventral thalamus	UBERON:0001897	84.98	gold quality
adult organism	UBERON:0007023	84.98	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.94	gold quality
upper lobe of lung	UBERON:0008948	84.79	gold quality
colonic mucosa	UBERON:0000317	84.45	gold quality
postcentral gyrus	UBERON:0002581	84.34	gold quality
upper lobe of left lung	UBERON:0008952	84.27	gold quality
parietal lobe	UBERON:0001872	84.01	gold quality
cortical plate	UBERON:0005343	83.99	gold quality
medulla oblongata	UBERON:0001896	83.98	gold quality
superior frontal gyrus	UBERON:0002661	83.96	gold quality
right lung	UBERON:0002167	83.80	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	25.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

280 targeting SNX30, 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-3613-3P	100.00	76.36	7965
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	snx30	ENSDARG00000069601
mus_musculus	Snx30	ENSMUSG00000028385
rattus_norvegicus	Snx30	ENSRNOG00000017132

Paralogs (15): SNX11 (ENSG00000002919), SNX1 (ENSG00000028528), SNX10 (ENSG00000086300), SNX5 (ENSG00000089006), SNX8 (ENSG00000106266), SNX3 (ENSG00000112335), SNX4 (ENSG00000114520), SNX6 (ENSG00000129515), SNX9 (ENSG00000130340), SNX12 (ENSG00000147164), SNX7 (ENSG00000162627), SNX32 (ENSG00000172803), SNX33 (ENSG00000173548), SNX18 (ENSG00000178996), SNX2 (ENSG00000205302)

Protein

Protein identifiers

Sorting nexin-30 — Q5VWJ9 (reviewed: Q5VWJ9)

All UniProt accessions (2): Q5VWJ9, H0Y496

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the regulation of endocytosis and in several stages of intracellular trafficking. Together with SNX4, involved in autophagosome assembly.

Subunit / interactions. Heterodimer; heterodimerizes with SNX4.

Subcellular location. Early endosome membrane.

Similarity. Belongs to the sorting nexin family.

RefSeq proteins (1): NP_001013012* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001683	PX_dom	Domain
IPR004148	BAR_dom	Domain
IPR027267	AH/BAR_dom_sf	Homologous_superfamily
IPR028649	SNX30_BAR	Domain
IPR036871	PX_dom_sf	Homologous_superfamily

Pfam: PF00787, PF03114

UniProt features (14 total): binding site 4, domain 2, modified residue 2, sequence variant 2, region of interest 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VWJ9-F1	81.33	0.64

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): 132; 134; 162; 176

Post-translational modifications (2): 38, 40

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 225 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GOBP_REGULATION_OF_AUTOPHAGY, GOBP_VACUOLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_VACUOLE_ORGANIZATION, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_VACUOLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_MACROAUTOPHAGY, MARTINEZ_RB1_TARGETS_UP, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_CATABOLIC_PROCESS, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, GOBP_ORGANELLE_ASSEMBLY

GO Biological Process (6): mitophagy (GO:0000423), protein transport (GO:0015031), endocytic recycling (GO:0032456), piecemeal microautophagy of the nucleus (GO:0034727), reticulophagy (GO:0061709), positive regulation of autophagosome assembly (GO:2000786)

GO Molecular Function (2): phosphatidylinositol binding (GO:0035091), protein binding (GO:0005515)

GO Cellular Component (7): phagophore assembly site (GO:0000407), early endosome (GO:0005769), early endosome membrane (GO:0031901), cytoplasm (GO:0005737), endosome (GO:0005768), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
macroautophagy	2
cytoplasm	2
autophagy of mitochondrion	1
transport	1
intracellular protein localization	1
establishment of protein localization	1
endosomal transport	1
vesicle-mediated transport to the plasma membrane	1
microautophagy	1
nucleophagy	1
nucleus disassembly	1
autophagosome assembly	1
positive regulation of macroautophagy	1
positive regulation of vacuole organization	1
positive regulation of organelle assembly	1
regulation of autophagosome assembly	1
anion binding	1
binding	1
endosome	1
early endosome	1
endosome membrane	1
intracellular anatomical structure	1
endomembrane system	1
cytoplasmic vesicle	1
intracellular vesicle	1

Protein interactions and networks

STRING

630 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNX30	MRPS35	P82673	541
SNX30	MIX23	Q4VC31	479
SNX30	QRICH1	Q2TAL8	435
SNX30	H3BQ15	H3BQ15	431
SNX30	AMDHD2	Q9Y303	419
SNX30	TMEM63A	O94886	413
SNX30	KGD4	P82909	400
SNX30	SCCPDH	Q8NBX0	399
SNX30	IRF2BP1	Q8IU81	392
SNX30	ATG12	O94817	367
SNX30	ANKS1A	Q92625	361
SNX30	BUD31	P41223	355
SNX30	PCBP3	P57721	350
SNX30	FKBP15	Q5T1M5	350
SNX30	SNX4	O95219	349

IntAct

19 interactions, top by confidence:

A	B	Type	Score
SNX4	SNX30	psi-mi:“MI:0914”(association)	0.830
SNX4	SNX30	psi-mi:“MI:0915”(physical association)	0.830
SNX30	SNX30	psi-mi:“MI:0915”(physical association)	0.400
SNX30	SNX32	psi-mi:“MI:0915”(physical association)	0.400
CAPZB	ENAH	psi-mi:“MI:0914”(association)	0.350
SNX4	SNX2	psi-mi:“MI:0914”(association)	0.350
MECR	SNX4	psi-mi:“MI:0914”(association)	0.350
C1orf210	IPO7	psi-mi:“MI:0914”(association)	0.350
PAAT	HIP1	psi-mi:“MI:0914”(association)	0.350
SNX4	HBB	psi-mi:“MI:0914”(association)	0.350
CEP43	RIPK2	psi-mi:“MI:2364”(proximity)	0.270
TGOLN2	BLTP3B	psi-mi:“MI:2364”(proximity)	0.270
FHIP1A	ILVBL	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (36): SNX30 (Proximity Label-MS), SNX30 (Affinity Capture-MS), SNX30 (Affinity Capture-RNA), SNX30 (Proximity Label-MS), SNX30 (Affinity Capture-RNA), SNX30 (Proximity Label-MS), SNX30 (Proximity Label-MS), SNX30 (Proximity Label-MS), SNX30 (Proximity Label-MS), SNX30 (Proximity Label-MS), SNX30 (Proximity Label-MS), SNX30 (Affinity Capture-MS), SNX30 (Affinity Capture-MS), SNX30 (Affinity Capture-MS), SNX30 (Affinity Capture-MS)

ESM2 similar proteins: A1A4L0, A6H6A9, B4F779, G5E8V9, O35382, O60890, O95219, P0CAX5, P53365, P53367, Q08DP6, Q28E02, Q3ZCL5, Q4V7P7, Q566W7, Q5EAD0, Q5R4C2, Q5RCW6, Q5T0N5, Q5VWJ9, Q5ZJ17, Q60437, Q62824, Q6AY65, Q6GMN2, Q6PCS4, Q6Y5D8, Q6ZQ82, Q7YQL5, Q7YQL6, Q80TY0, Q8BHY8, Q8BKX1, Q8CE50, Q8K221, Q8K3G9, Q8K3H0, Q8N6S4, Q8NEU8, Q8R511

Diamond homologs: B9DFS6, I1RXT2, O14243, O60493, O60749, O70492, O94291, P0C220, P0CR58, P0CR59, P0CR62, P0CR63, P47057, Q1RMH8, Q28E02, Q4I1H6, Q4R5U9, Q4V7P7, Q566W7, Q5R5V1, Q5R9A9, Q5U211, Q5VWJ9, Q7SH92, Q8CE50, Q8L5Z7, Q9CWK8, Q9CY18, Q9P779, Q9UNH6, A0A1B7YDZ4, O60107, O70493, P0CR60, P0CR61, Q08DD7, Q2TBW7, Q2U4K2, Q4P1V3, Q4PHC3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	57
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
145648	GRCh38/hg38 9q31.1-32(chr9:103767420-112984794)x1	Pathogenic

SpliceAI

2278 predictions. Top by Δscore:

Variant	Effect	Δscore
9:112804772:TTAG:T	acceptor_loss	1.0000
9:112804774:A:AG	acceptor_gain	1.0000
9:112804774:A:T	acceptor_loss	1.0000
9:112804774:AG:A	acceptor_gain	1.0000
9:112804775:G:A	acceptor_loss	1.0000
9:112804775:G:GG	acceptor_gain	1.0000
9:112804775:GG:G	acceptor_gain	1.0000
9:112804966:AA:A	donor_gain	1.0000
9:112804966:AAG:A	donor_loss	1.0000
9:112804967:AG:A	donor_loss	1.0000
9:112804968:G:GG	donor_gain	1.0000
9:112804968:G:T	donor_loss	1.0000
9:112804969:TA:T	donor_loss	1.0000
9:112816484:G:GT	donor_gain	1.0000
9:112816485:A:T	donor_gain	1.0000
9:112817700:TGCA:T	acceptor_loss	1.0000
9:112817701:GCA:G	acceptor_loss	1.0000
9:112817702:CAG:C	acceptor_gain	1.0000
9:112817703:A:AG	acceptor_gain	1.0000
9:112817703:AGA:A	acceptor_gain	1.0000
9:112817703:AGAG:A	acceptor_loss	1.0000
9:112817704:G:GA	acceptor_gain	1.0000
9:112817704:GA:G	acceptor_gain	1.0000
9:112817704:GAG:G	acceptor_gain	1.0000
9:112817704:GAGT:G	acceptor_gain	1.0000
9:112817704:GAGTA:G	acceptor_gain	1.0000
9:112817786:G:GT	donor_gain	1.0000
9:112817816:G:GG	donor_gain	1.0000
9:112817818:AGGTA:A	donor_gain	1.0000
9:112817819:GGTAG:G	donor_gain	1.0000

AlphaMissense

2875 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:112804903:T:A	V95D	1.000
9:112817751:G:C	R132T	1.000
9:112817751:G:T	R132I	1.000
9:112817752:A:C	R132S	1.000
9:112817752:A:T	R132S	1.000
9:112817753:T:G	Y133D	1.000
9:112817784:T:C	L143P	1.000
9:112830732:C:A	P156H	1.000
9:112830740:T:C	F159L	1.000
9:112830742:T:A	F159L	1.000
9:112830742:T:G	F159L	1.000
9:112830767:T:C	F168L	1.000
9:112830769:T:A	F168L	1.000
9:112830769:T:G	F168L	1.000
9:112830779:T:C	F172L	1.000
9:112830781:T:A	F172L	1.000
9:112830781:T:G	F172L	1.000
9:112830791:A:G	R176G	1.000
9:112830792:G:C	R176T	1.000
9:112830792:G:T	R176I	1.000
9:112830793:A:C	R176S	1.000
9:112830793:A:T	R176S	1.000
9:112830804:T:C	L180S	1.000
9:112830804:T:G	L180W	1.000
9:112836389:G:C	R265P	1.000
9:112804950:T:G	Y111D	0.999
9:112817748:G:C	R131P	0.999
9:112817750:A:G	R132G	0.999
9:112817753:T:C	Y133H	0.999
9:112817754:A:G	Y133C	0.999

dbSNP variants (sampled 300 via entrez): RS1000042721 (9:112830548 G>T), RS1000056041 (9:112869149 G>A,T), RS1000079018 (9:112783302 T>C), RS1000095728 (9:112789602 A>G), RS1000097448 (9:112829923 A>G), RS1000103008 (9:112836595 C>G,T), RS1000106530 (9:112868900 G>A), RS1000132359 (9:112844598 G>C), RS1000138020 (9:112783600 C>G), RS1000141633 (9:112877465 A>G), RS1000161250 (9:112842837 C>T), RS1000248412 (9:112840995 C>G), RS1000284024 (9:112788996 A>G), RS1000286037 (9:112777905 C>A,T), RS1000298487 (9:112795771 A>T)

Disease associations

OMIM: gene MIM:620955 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST006257_2	Elevated fasting plasma glucose	3.000000e-06
GCST006273_3	Diastolic blood pressure night-to-day ratio in hypertension	6.000000e-06
GCST009391_1094	Metabolite levels	5.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006945	diastolic blood pressure change measurement
EFO:0010446	2-hydroxyglutaric acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, affects methylation, decreases expression, decreases methylation	5
daidzein	affects cotreatment, decreases expression	1
bisphenol A	increases expression	1
daidzin	affects cotreatment, decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
genistin	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
glycitein	affects cotreatment, decreases expression	1
monomethylarsonous acid	increases expression	1
glycitin	affects cotreatment, decreases expression	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Cadmium	increases abundance, increases expression	1
Caffeine	affects phosphorylation	1
Calcitriol	increases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Rotenone	decreases expression	1
Urethane	increases expression	1
Valproic Acid	increases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Palmitic Acid	decreases expression	1
Genistein	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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