Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	29887
Gene name	Sorting nexin 10
Gene symbol	SNX10
Synonyms (NCBI Gene)	OPTB8
Chromosome	7
Chromosome location	7p15.2
Summary	This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like

Show/Hide all (5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs377321694	T>A,C	Pathogenic	Synonymous variant, coding sequence variant, intron variant, stop gained
rs398123011	G>A	Pathogenic	Missense variant, coding sequence variant, intron variant
rs587777490	C>T	Pathogenic	Coding sequence variant, genic upstream transcript variant, stop gained
rs897553060	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1353879401	C>T	Likely-pathogenic	Coding sequence variant, intron variant, stop gained

135

Show/Hide all (135)

miRTarBase ID	miRNA	Experiments	Reference
MIRT024587	hsa-miR-215-5p	Microarray	19074876
MIRT026783	hsa-miR-192-5p	Microarray	19074876
MIRT543820	hsa-miR-6507-5p	PAR-CLIP	21572407
MIRT103410	hsa-miR-126-5p	PAR-CLIP	21572407
MIRT543819	hsa-miR-3928-5p	PAR-CLIP	21572407
MIRT543818	hsa-miR-6806-3p	PAR-CLIP	21572407
MIRT392899	hsa-miR-27b-5p	PAR-CLIP	21572407
MIRT543817	hsa-miR-3160-5p	PAR-CLIP	21572407
MIRT543816	hsa-miR-496	PAR-CLIP	21572407
MIRT543815	hsa-miR-331-5p	PAR-CLIP	21572407
MIRT320304	hsa-miR-4795-3p	PAR-CLIP	21572407
MIRT543814	hsa-miR-127-5p	PAR-CLIP	21572407
MIRT320305	hsa-miR-6509-5p	PAR-CLIP	21572407
MIRT543813	hsa-miR-6830-3p	PAR-CLIP	21572407
MIRT497249	hsa-miR-1252-5p	PAR-CLIP	22291592
MIRT497248	hsa-miR-1301-5p	PAR-CLIP	22291592
MIRT497247	hsa-miR-6502-5p	PAR-CLIP	22291592
MIRT103433	hsa-miR-92a-3p	HITS-CLIP	22473208
MIRT103438	hsa-miR-92b-3p	HITS-CLIP	22473208
MIRT103432	hsa-miR-32-5p	HITS-CLIP	22473208
MIRT543820	hsa-miR-6507-5p	PAR-CLIP	21572407
MIRT103410	hsa-miR-126-5p	PAR-CLIP	21572407
MIRT543819	hsa-miR-3928-5p	PAR-CLIP	21572407
MIRT543818	hsa-miR-6806-3p	PAR-CLIP	21572407
MIRT392899	hsa-miR-27b-5p	PAR-CLIP	21572407
MIRT543817	hsa-miR-3160-5p	PAR-CLIP	21572407
MIRT543816	hsa-miR-496	PAR-CLIP	21572407
MIRT543815	hsa-miR-331-5p	PAR-CLIP	21572407
MIRT320304	hsa-miR-4795-3p	PAR-CLIP	21572407
MIRT543814	hsa-miR-127-5p	PAR-CLIP	21572407
MIRT320305	hsa-miR-6509-5p	PAR-CLIP	21572407
MIRT543813	hsa-miR-6830-3p	PAR-CLIP	21572407
MIRT497249	hsa-miR-1252-5p	PAR-CLIP	22291592
MIRT497248	hsa-miR-1301-5p	PAR-CLIP	22291592
MIRT497247	hsa-miR-6502-5p	PAR-CLIP	22291592
MIRT1376657	hsa-miR-1202	CLIP-seq
MIRT1376658	hsa-miR-1245	CLIP-seq
MIRT1376659	hsa-miR-148a	CLIP-seq
MIRT1376660	hsa-miR-148b	CLIP-seq
MIRT1376661	hsa-miR-152	CLIP-seq
MIRT1376662	hsa-miR-1825	CLIP-seq
MIRT1376663	hsa-miR-1909	CLIP-seq
MIRT1376664	hsa-miR-202	CLIP-seq
MIRT1376665	hsa-miR-2052	CLIP-seq
MIRT1376666	hsa-miR-3591-3p	CLIP-seq
MIRT1376667	hsa-miR-3972	CLIP-seq
MIRT1376668	hsa-miR-4255	CLIP-seq
MIRT1376669	hsa-miR-4422	CLIP-seq
MIRT1376670	hsa-miR-4724-5p	CLIP-seq
MIRT1376671	hsa-miR-4766-5p	CLIP-seq
MIRT1376672	hsa-miR-4776-3p	CLIP-seq
MIRT1376673	hsa-miR-622	CLIP-seq
MIRT1376674	hsa-miR-3168	CLIP-seq
MIRT1376675	hsa-miR-338-5p	CLIP-seq
MIRT1376676	hsa-miR-369-3p	CLIP-seq
MIRT1376677	hsa-miR-374c	CLIP-seq
MIRT1376678	hsa-miR-4264	CLIP-seq
MIRT1376679	hsa-miR-4328	CLIP-seq
MIRT1376680	hsa-miR-4427	CLIP-seq
MIRT1376681	hsa-miR-4517	CLIP-seq
MIRT1376682	hsa-miR-4662a-3p	CLIP-seq
MIRT1376683	hsa-miR-4666-3p	CLIP-seq
MIRT1376684	hsa-miR-4680-3p	CLIP-seq
MIRT1376685	hsa-miR-4762-3p	CLIP-seq
MIRT1376686	hsa-miR-4797-3p	CLIP-seq
MIRT1376687	hsa-miR-582-5p	CLIP-seq
MIRT1376688	hsa-miR-593	CLIP-seq
MIRT1376689	hsa-miR-654-3p	CLIP-seq
MIRT1376690	hsa-miR-655	CLIP-seq
MIRT1376691	hsa-miR-656	CLIP-seq
MIRT1376692	hsa-miR-664	CLIP-seq
MIRT1376693	hsa-miR-889	CLIP-seq
MIRT1376694	hsa-miR-3684	CLIP-seq
MIRT1376695	hsa-miR-4282	CLIP-seq
MIRT1376696	hsa-miR-4698	CLIP-seq
MIRT1376697	hsa-miR-4699-3p	CLIP-seq
MIRT1376698	hsa-miR-520d-5p	CLIP-seq
MIRT1376699	hsa-miR-524-5p	CLIP-seq
MIRT1376657	hsa-miR-1202	CLIP-seq
MIRT1376700	hsa-miR-1297	CLIP-seq
MIRT1376659	hsa-miR-148a	CLIP-seq
MIRT1376660	hsa-miR-148b	CLIP-seq
MIRT1376661	hsa-miR-152	CLIP-seq
MIRT1376662	hsa-miR-1825	CLIP-seq
MIRT1376663	hsa-miR-1909	CLIP-seq
MIRT1376664	hsa-miR-202	CLIP-seq
MIRT1376665	hsa-miR-2052	CLIP-seq
MIRT1376701	hsa-miR-26a	CLIP-seq
MIRT1376702	hsa-miR-26b	CLIP-seq
MIRT1376703	hsa-miR-27a	CLIP-seq
MIRT1376704	hsa-miR-27b	CLIP-seq
MIRT1376705	hsa-miR-3074-3p	CLIP-seq
MIRT1376706	hsa-miR-3144-3p	CLIP-seq
MIRT1376707	hsa-miR-3200-5p	CLIP-seq
MIRT1376708	hsa-miR-3617	CLIP-seq
MIRT1376709	hsa-miR-3647-3p	CLIP-seq
MIRT1376667	hsa-miR-3972	CLIP-seq
MIRT1376668	hsa-miR-4255	CLIP-seq
MIRT1376669	hsa-miR-4422	CLIP-seq
MIRT1376710	hsa-miR-4465	CLIP-seq
MIRT1376671	hsa-miR-4766-5p	CLIP-seq
MIRT1376672	hsa-miR-4776-3p	CLIP-seq
MIRT1376711	hsa-miR-513a-5p	CLIP-seq
MIRT1376712	hsa-miR-641	CLIP-seq
MIRT1376705	hsa-miR-3074-3p	CLIP-seq
MIRT2112067	hsa-miR-3163	CLIP-seq
MIRT2112068	hsa-miR-4495	CLIP-seq
MIRT2112069	hsa-miR-4668-3p	CLIP-seq
MIRT2112070	hsa-miR-500a	CLIP-seq
MIRT1376679	hsa-miR-4328	CLIP-seq
MIRT2112071	hsa-miR-4652-3p	CLIP-seq
MIRT2335296	hsa-miR-1290	CLIP-seq
MIRT1376659	hsa-miR-148a	CLIP-seq
MIRT1376660	hsa-miR-148b	CLIP-seq
MIRT1376661	hsa-miR-152	CLIP-seq
MIRT1376662	hsa-miR-1825	CLIP-seq
MIRT1376663	hsa-miR-1909	CLIP-seq
MIRT1376664	hsa-miR-202	CLIP-seq
MIRT1376703	hsa-miR-27a	CLIP-seq
MIRT1376704	hsa-miR-27b	CLIP-seq
MIRT1376682	hsa-miR-4662a-3p	CLIP-seq
MIRT1376670	hsa-miR-4724-5p	CLIP-seq
MIRT1376671	hsa-miR-4766-5p	CLIP-seq
MIRT1376711	hsa-miR-513a-5p	CLIP-seq
MIRT2335297	hsa-miR-630	CLIP-seq
MIRT2335298	hsa-miR-944	CLIP-seq
MIRT2629313	hsa-miR-1225-5p	CLIP-seq
MIRT2629314	hsa-miR-1255a	CLIP-seq
MIRT2629315	hsa-miR-1255b	CLIP-seq
MIRT2629316	hsa-miR-421	CLIP-seq
MIRT2629317	hsa-miR-4272	CLIP-seq
MIRT2629318	hsa-miR-4738-3p	CLIP-seq
MIRT2629319	hsa-miR-4802-3p	CLIP-seq
MIRT2629320	hsa-miR-490-5p	CLIP-seq
MIRT2629321	hsa-miR-555	CLIP-seq

Show/Hide all (44)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001696	Process	Gastric acid secretion	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 32296183, 32814053
GO:0005545	Function	1-phosphatidylinositol binding	IMP	17012226
GO:0005634	Component	Nucleus	IDA	22174188
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IBA
GO:0005768	Component	Endosome	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA	22174188
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005813	Component	Centrosome	IDA	21844891
GO:0005813	Component	Centrosome	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0006886	Process	Intracellular protein transport	IEA
GO:0006897	Process	Endocytosis	IEA
GO:0007032	Process	Endosome organization	IMP	17012226
GO:0008289	Function	Lipid binding	IEA
GO:0010008	Component	Endosome membrane	IEA
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016050	Process	Vesicle organization	IBA
GO:0016050	Process	Vesicle organization	IEA
GO:0019725	Process	Cellular homeostasis	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0030141	Component	Secretory granule	IEA
GO:0030316	Process	Osteoclast differentiation	IEA
GO:0030316	Process	Osteoclast differentiation	ISS
GO:0031313	Component	Extrinsic component of endosome membrane	IDA	17012226
GO:0035091	Function	Phosphatidylinositol binding	IEA
GO:0035630	Process	Bone mineralization involved in bone maturation	IEA
GO:0044691	Process	Tooth eruption	IEA
GO:0045453	Process	Bone resorption	IEA
GO:0046849	Process	Bone remodeling	IEA
GO:0051117	Function	ATPase binding	IPI	21844891
GO:0051649	Process	Establishment of localization in cell	IEA
GO:0055074	Process	Calcium ion homeostasis	IEA
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IMP	21844891
GO:0061512	Process	Protein localization to cilium	IMP	21844891
GO:0071539	Process	Protein localization to centrosome	IMP	21844891
GO:0090651	Component	Apical cytoplasm	IEA
GO:0097178	Process	Ruffle assembly	IEA
GO:1901981	Function	Phosphatidylinositol phosphate binding	IBA
GO:1990830	Process	Cellular response to leukemia inhibitory factor	IEA

MIM	HGNC	e!Ensembl
614780	14974	ENSG00000086300

Q9Y5X0

Protein name

Sorting nexin-10

Protein function

Probable phosphoinositide-binding protein involved in protein sorting and membrane trafficking in endosomes. Plays a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium. Required for the l

PDB

4ON3 , 4PZG , 6KOK

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00787	PX	40 → 124	PX domain	Domain

Sequence

MFPEQQKEEFVSVWVRDPRIQKEDFWHSYIDYEICIHTNSMCFTMKTSCVRRRYREFVWL
RQRLQSNALLVQLPELPSKNLFFNMNNRQHVDQRRQGLEDFLRKVLQNALLLSDSSLHLF
LQSHLNSEDIEACVSGQTKYSVEEAIHKFALMNRRFPEEDEEGKKENDIDYDSESSSSGL
GHSSDDSSSHGCKVNTAPQES

Sequence length

201

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive osteopetrosis 8	Pathogenic; Likely pathogenic	rs587777490, rs2536153865, rs398123011, rs1353879401	RCV000128452 RCV003444394 RCV000033149 RCV000991381	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Gastric cancer	Likely pathogenic	rs776348160	RCV005922844	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (23)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE OSTEOPETROSIS	—	Disgenet Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DENTAL CARIES	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Infantile osteopetrosis	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOPETROSIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOPETROSIS, AUTOSOMAL RECESSIVE 8	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SNX10-related disorder	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (16)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Atrial Fibrillation	Associate	33594863	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Associate	34116656	★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Associate	26631031	★★★★★ ★☆☆☆☆ Found in Text Mining only
Fibrosis	Associate	33594863	★★★★★ ★☆☆☆☆ Found in Text Mining only
Heart Diseases	Associate	33594863	★★★★★ ★☆☆☆☆ Found in Text Mining only
Heart Valve Diseases	Associate	33594863	★★★★★ ★☆☆☆☆ Found in Text Mining only
Inflammation	Associate	31356157	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasm Metastasis	Associate	34511489	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	26631031, 30487700, 34116656	★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteopetrosis	Associate	28592808, 30885997, 39875016	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteopetrosis mild autosomal recessive form	Associate	23280965, 28592808, 28816234, 29034896, 36526684	★★★★★ ★☆☆☆☆ Found in Text Mining only
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	39453390	★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Associate	33672425	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Associate	30487700	★★★★★ ★☆☆☆☆ Found in Text Mining only
Tuberculosis Pulmonary	Associate	35720382	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Associate	34116656	★★★★★ ★☆☆☆☆ Found in Text Mining only

SNX10 (sorting nexin 10)