SNX18

sorting nexin 18, the group of PX-BAR domain containing|Sorting nexins

Basic information

Region (hg38): 5:54517759-54546586

Previous symbols: [ "SNAG1" ]

Links

ENSG00000178996 ∙ NCBI:112574 ∙ ∙ HGNC:19245 ∙ Uniprot:Q96RF0 ∙ 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 SNX18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX18 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					2	2
missense			31		1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8			8
Total	0	0	39	0	3

Variants in SNX18

This is a list of pathogenic ClinVar variants found in the SNX18 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-54517986-A-G		not specified	Uncertain significance (May 17, 2023)
5-54518076-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-54518076-G-C		not specified	Uncertain significance (Mar 25, 2022)
5-54518110-C-T		not specified	Uncertain significance (May 23, 2023)
5-54518125-T-A		not specified	Uncertain significance (Nov 21, 2023)
5-54518167-C-T		not specified	Uncertain significance (Jan 02, 2024)
5-54518176-C-T		not specified	Uncertain significance (Dec 16, 2022)
5-54518191-A-G		not specified	Uncertain significance (Jun 03, 2022)
5-54518230-C-G		not specified	Uncertain significance (Jun 24, 2022)
5-54518230-C-T		not specified	Uncertain significance (Mar 29, 2022)
5-54518284-A-G		not specified	Uncertain significance (May 26, 2022)
5-54518290-C-T		not specified	Uncertain significance (Jan 03, 2024)
5-54518298-C-G		not specified	Uncertain significance (Jun 03, 2022)
5-54518317-C-T		not specified	Uncertain significance (Sep 01, 2021)
5-54518325-G-A		not specified	Uncertain significance (Mar 02, 2023)
5-54518331-C-A		not specified	Uncertain significance (Dec 17, 2023)
5-54518332-C-G		not specified	Uncertain significance (Jul 20, 2021)
5-54518415-G-A		not specified	Uncertain significance (Jan 23, 2024)
5-54518447-G-C			Benign (Feb 26, 2018)
5-54518523-G-A		not specified	Uncertain significance (Mar 31, 2024)
5-54518581-T-A		not specified	Uncertain significance (Jun 24, 2022)
5-54518620-C-T		not specified	Uncertain significance (May 13, 2024)
5-54518641-A-G		not specified	Uncertain significance (Apr 01, 2024)
5-54518831-G-A			Benign (May 14, 2018)
5-54518880-C-T		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX18	protein_coding	protein_coding	ENST00000326277	1	28827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.956	0.0436	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	257	363	0.709	0.0000222	3995
Missense in Polyphen		61	135.38	0.45057		1509
Synonymous	-0.147	180	178	1.01	0.0000133	1241
Loss of Function	3.25	1	14.2	0.0703	6.15e-7	155

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in endocytosis and intracellular vesicle trafficking, both during interphase and at the end of mitosis. Required for efficient progress through mitosis and cytokinesis. Required for normal formation of the cleavage furrow at the end of mitosis. Plays a role in endocytosis via clathrin-coated pits, but also clathrin-independent, actin-dependent fluid-phase endocytosis. Plays a role in macropinocytosis. Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate and promotes membrane tubulation. Stimulates the GTPase activity of DNM2. Promotes DNM2 location at the plasma membrane. {ECO:0000269|PubMed:18411244, ECO:0000269|PubMed:20427313, ECO:0000269|PubMed:21048941, ECO:0000269|PubMed:22718350}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• loftool: 0.583
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.71

Haploinsufficiency Scores

• pHI: 0.258
• hipred: Y
• hipred_score: 0.538
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx18

Gene ontology

• Biological process: mitotic cytokinesis;endocytosis;protein transport;endosomal transport;cleavage furrow formation;positive regulation of GTPase activity
• Cellular component: endosome membrane;clathrin-coated vesicle;cytoplasmic vesicle membrane;extrinsic component of cytoplasmic side of plasma membrane;cytoplasmic vesicle;extracellular exosome
• Molecular function: protein binding;phosphatidylinositol-4,5-bisphosphate binding