SNX15

sorting nexin 15, the group of Sorting nexins

Basic information

Region (hg38): 11:65027439-65040572

Links

ENSG00000110025 ∙ NCBI:29907 ∙ OMIM:605964 ∙ HGNC:14978 ∙ Uniprot:Q9NRS6 ∙ 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 SNX15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX15 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in SNX15

This is a list of pathogenic ClinVar variants found in the SNX15 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65027625-G-C		not specified	Uncertain significance (Dec 15, 2022)
11-65032183-G-C		not specified	Uncertain significance (Sep 04, 2024)
11-65032452-A-G		not specified	Uncertain significance (Jun 29, 2023)
11-65032455-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-65032461-C-A		not specified	Uncertain significance (Feb 28, 2024)
11-65032495-G-A		not specified	Uncertain significance (Feb 28, 2024)
11-65032518-G-A		not specified	Uncertain significance (Sep 30, 2024)
11-65034865-T-G		not specified	Uncertain significance (May 08, 2024)
11-65034876-C-T		not specified	Uncertain significance (Jun 06, 2023)
11-65034904-G-A		not specified	Uncertain significance (Aug 22, 2022)
11-65034922-C-G		not specified	Uncertain significance (Jan 23, 2023)
11-65035116-C-A		not specified	Uncertain significance (Mar 07, 2024)
11-65035116-C-T		not specified	Uncertain significance (May 31, 2022)
11-65035138-C-G		not specified	Uncertain significance (Dec 16, 2023)
11-65035150-G-A		not specified	Uncertain significance (Sep 13, 2023)
11-65035158-C-G		not specified	Uncertain significance (May 30, 2024)
11-65035170-G-A		not specified	Uncertain significance (Jul 05, 2024)
11-65035529-C-T		not specified	Uncertain significance (Oct 26, 2022)
11-65035645-G-T		not specified	Uncertain significance (Aug 02, 2021)
11-65038587-G-C		not specified	Uncertain significance (Feb 17, 2024)
11-65038596-A-C		not specified	Uncertain significance (May 28, 2024)
11-65038613-A-G		not specified	Likely benign (May 04, 2022)
11-65038707-C-T		not specified	Uncertain significance (Sep 21, 2023)
11-65038733-A-C		not specified	Uncertain significance (Sep 03, 2024)
11-65038773-C-T		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX15	protein_coding	protein_coding	ENST00000377244	8	13165

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000397	0.836	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.874	170	205	0.828	0.0000124	2165
Missense in Polyphen		75	86.022	0.87187		825
Synonymous	1.20	70	84.0	0.833	0.00000473	710
Loss of Function	1.40	11	17.3	0.637	0.00000105	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000199	0.000188
Ashkenazi Jewish	0.000350	0.000298
East Asian	0.000109	0.000109
Finnish	0.000671	0.000647
European (Non-Finnish)	0.000253	0.000229
Middle Eastern	0.000109	0.000109
South Asian	0.000114	0.0000980
Other	0.000176	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in several stages of intracellular trafficking. Overexpression of SNX15 disrupts the normal trafficking of proteins from the plasma membrane to recycling endosomes or the TGN. {ECO:0000269|PubMed:11085978}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.828
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• pHI: 0.179
• hipred: N
• hipred_score: 0.199
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.688

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx15
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: intracellular protein transport
• Cellular component: nucleolus;cytosol;membrane;cytoplasmic vesicle membrane
• Molecular function: protein binding;phosphatidylinositol binding