SNX2

sorting nexin 2, the group of PX-BAR domain containing|Sorting nexins

Basic information

Region (hg38): 5:122775079-122834543

Links

ENSG00000205302 ∙ NCBI:6643 ∙ OMIM:605929 ∙ HGNC:11173 ∙ Uniprot:O60749 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in SNX2

This is a list of pathogenic ClinVar variants found in the SNX2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-122775108-C-T		not specified	Uncertain significance (Jul 16, 2024)
5-122775115-G-C		not specified	Uncertain significance (Jun 23, 2021)
5-122775117-G-A		not specified	Uncertain significance (Mar 23, 2023)
5-122775119-G-A		not specified	Uncertain significance (Jun 02, 2023)
5-122775123-C-G		not specified	Uncertain significance (Feb 21, 2024)
5-122775135-G-T		not specified	Uncertain significance (Jun 27, 2022)
5-122775140-G-A		not specified	Uncertain significance (Jun 12, 2023)
5-122775167-G-A		not specified	Uncertain significance (Mar 20, 2023)
5-122799730-G-A		not specified	Uncertain significance (Jan 31, 2023)
5-122799734-C-T		not specified	Uncertain significance (May 01, 2024)
5-122799770-C-T		not specified	Uncertain significance (Sep 21, 2023)
5-122799829-G-A		not specified	Uncertain significance (Jul 16, 2024)
5-122801878-G-A		not specified	Uncertain significance (Mar 30, 2024)
5-122801900-A-T		not specified	Uncertain significance (Jul 25, 2023)
5-122803505-T-A		not specified	Uncertain significance (Jun 28, 2022)
5-122815904-A-G		not specified	Uncertain significance (Nov 28, 2023)
5-122816942-C-G		not specified	Uncertain significance (Jan 04, 2024)
5-122816985-A-G		not specified	Uncertain significance (May 01, 2024)
5-122817371-A-G		not specified	Uncertain significance (Aug 15, 2024)
5-122818879-T-A		not specified	Uncertain significance (Nov 17, 2022)
5-122818946-C-A		not specified	Uncertain significance (Jul 27, 2024)
5-122818971-A-G		not specified	Uncertain significance (May 15, 2023)
5-122819018-G-C		not specified	Uncertain significance (Aug 14, 2024)
5-122826050-G-A		not specified	Uncertain significance (Dec 16, 2023)
5-122827392-T-C		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX2	protein_coding	protein_coding	ENST00000379516	15	55113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0154	125720	0	14	125734	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.596	238	265	0.897	0.0000126	3417
Missense in Polyphen		94	99.337	0.94627		1310
Synonymous	-0.500	96	90.0	1.07	0.00000467	944
Loss of Function	4.43	4	30.3	0.132	0.00000152	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000981	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000659	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in several stages of intracellular trafficking. Interacts with membranes containing phosphatidylinositol 3- phosphate (PtdIns(3P)) or phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) (PubMed:16179610). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex (PubMed:17101778). The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC) (Probable). Can sense membrane curvature and has in vitro vesicle-to-membrane remodeling activity (PubMed:23085988). Required for retrograde endosome-to-TGN transport of TGN38 (PubMed:20138391). Promotes KALRN- and RHOG-dependent but retromer-independent membrane remodeling such as lamellipodium formation; the function is dependent on GEF activity of KALRN (PubMed:20604901). {ECO:0000269|PubMed:16179610, ECO:0000269|PubMed:17101778, ECO:0000269|PubMed:20138391, ECO:0000269|PubMed:20604901, ECO:0000269|PubMed:23085988, ECO:0000303|PubMed:16179610}.
• Pathway: Endocytosis - Homo sapiens (human);Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;TGF_beta_Receptor;PAR1-mediated thrombin signaling events (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.370
• rvis_EVS: -0.69
• rvis_percentile_EVS: 14.97

Haploinsufficiency Scores

• pHI: 0.339
• hipred: Y
• hipred_score: 0.783
• ghis: 0.674

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.349

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Snx2
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: intracellular protein transport;endocytosis;early endosome to Golgi transport;retrograde transport, endosome to Golgi;protein complex oligomerization;lamellipodium morphogenesis
• Cellular component: cytoplasm;lysosome;endosome;cytosol;endosome membrane;membrane;lamellipodium;retromer complex;retromer, tubulation complex;early endosome membrane;protein-containing complex
• Molecular function: epidermal growth factor receptor binding;insulin receptor binding;protein binding;phosphatidylinositol binding;protein homodimerization activity;cadherin binding;protein heterodimerization activity;transferrin receptor binding;leptin receptor binding