SNX16

sorting nexin 16, the group of Sorting nexins

Basic information

Region (hg38): 8:81799580-81842866

Links

ENSG00000104497 ∙ NCBI:64089 ∙ OMIM:614903 ∙ HGNC:14980 ∙ Uniprot:P57768 ∙ 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 SNX16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX16 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in SNX16

This is a list of pathogenic ClinVar variants found in the SNX16 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-81801564-C-T		not specified	Uncertain significance (Aug 14, 2023)
8-81801565-T-C		not specified	Uncertain significance (Sep 14, 2022)
8-81801580-G-T		not specified	Uncertain significance (Dec 19, 2023)
8-81801584-A-T		not specified	Uncertain significance (Feb 27, 2023)
8-81801591-G-C		not specified	Uncertain significance (Sep 30, 2021)
8-81801592-C-G		not specified	Uncertain significance (Nov 09, 2022)
8-81802417-G-C		not specified	Uncertain significance (May 09, 2023)
8-81803105-C-G		not specified	Uncertain significance (Apr 19, 2023)
8-81803176-A-G		not specified	Uncertain significance (Sep 28, 2022)
8-81803209-T-C		not specified	Uncertain significance (Apr 06, 2023)
8-81815353-C-T		not specified	Uncertain significance (Mar 07, 2023)
8-81815375-G-C		not specified	Uncertain significance (Mar 03, 2022)
8-81823805-C-T		not specified	Uncertain significance (Dec 15, 2022)
8-81823859-C-T		not specified	Uncertain significance (Apr 08, 2024)
8-81823876-T-C		not specified	Uncertain significance (Sep 27, 2021)
8-81839649-A-G		not specified	Uncertain significance (Mar 27, 2023)
8-81839683-T-C		not specified	Uncertain significance (Jun 02, 2023)
8-81839701-G-T		not specified	Uncertain significance (Apr 12, 2023)
8-81839788-C-T		not specified	Uncertain significance (Aug 30, 2021)
8-81839793-G-A		not specified	Uncertain significance (Dec 16, 2023)
8-81839802-T-G		not specified	Uncertain significance (Oct 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX16	protein_coding	protein_coding	ENST00000396330	7	43286

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.42e-11	0.0284	125687	0	34	125721	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.987	127	162	0.782	0.00000746	2256
Missense in Polyphen		24	45.762	0.52445		678
Synonymous	-0.344	60	56.7	1.06	0.00000270	624
Loss of Function	-0.281	16	14.8	1.08	6.88e-7	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000649	0.000640
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000106
Middle Eastern	0.00	0.00
South Asian	0.000309	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in several stages of intracellular trafficking. Plays a role in protein transport from early to late endosomes. Plays a role in protein transport to the lysosome. Promotes degradation of EGFR after EGF signaling. Plays a role in intracellular transport of vesicular stomatitis virus nucleocapsids from the endosome to the cytoplasm. {ECO:0000269|PubMed:12813048, ECO:0000269|PubMed:15951806}.

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.959
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.580
• hipred: N
• hipred_score: 0.251
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx16

Gene ontology

• Biological process: protein targeting to lysosome;endosome to lysosome transport;negative regulation of ATPase activity;regulation of membrane potential;negative regulation of ion transport;early endosome to late endosome transport
• Cellular component: cytoplasm;lysosome;early endosome;late endosome;cytosol;plasma membrane;extrinsic component of endosome membrane;early endosome membrane;late endosome membrane;intracellular membrane-bounded organelle
• Molecular function: phosphatidylinositol binding;identical protein binding