SNX20

sorting nexin 20, the group of Sorting nexins

Basic information

Region (hg38): 16:50666299-50681353

Links

ENSG00000167208 ∙ NCBI:124460 ∙ OMIM:613281 ∙ HGNC:30390 ∙ Uniprot:Q7Z614 ∙ 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 SNX20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX20 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					1	1
missense			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	11	2	1

Variants in SNX20

This is a list of pathogenic ClinVar variants found in the SNX20 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-50669146-C-T		not specified	Uncertain significance (Aug 12, 2021)
16-50673490-C-G		not specified	Uncertain significance (May 27, 2022)
16-50673503-A-G		not specified	Uncertain significance (Jan 10, 2023)
16-50673542-G-A		not specified	Uncertain significance (Oct 20, 2021)
16-50673545-T-A		not specified	Uncertain significance (Oct 12, 2021)
16-50673591-G-A		not specified	Likely benign (Mar 21, 2024)
16-50673912-A-G		not specified	Uncertain significance (Jan 02, 2024)
16-50673942-C-T		not specified	Uncertain significance (Dec 16, 2023)
16-50673995-G-T		not specified	Likely benign (Apr 13, 2022)
16-50674023-C-T		not specified	Likely benign (Jul 30, 2023)
16-50675795-T-C		not specified	Uncertain significance (May 18, 2023)
16-50675843-C-T		not specified	Uncertain significance (Feb 28, 2024)
16-50675881-C-T			Benign (Jan 30, 2018)
16-50677444-G-T		not specified	Uncertain significance (Jan 03, 2022)
16-50677457-G-C		not specified	Uncertain significance (Apr 08, 2024)
16-50677468-G-T		not specified	Uncertain significance (Feb 10, 2023)
16-50677508-G-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX20	protein_coding	protein_coding	ENST00000330943	3	15054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000128	0.398	125723	0	18	125741	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	169	210	0.804	0.0000159	1991
Missense in Polyphen		38	61.952	0.61338		627
Synonymous	1.55	70	88.6	0.790	0.00000634	670
Loss of Function	0.357	8	9.17	0.873	3.90e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000241	0.000238
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000546	0.0000527
Middle Eastern	0.0000546	0.0000544
South Asian	0.000100	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cellular vesicle trafficking. Has been proposed to function as a sorting protein that targets SELPLG into endosomes, but has no effect on SELPLG internalization from the cell surface, or on SELPLG-mediated cell-cell adhesion. {ECO:0000305|PubMed:18196517}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.814
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.319
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.470

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx20
• Phenotype: normal phenotype

Gene ontology

• Biological process: protein transport
• Cellular component: nucleoplasm;plasma membrane;early endosome membrane
• Molecular function: protein binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-3-phosphate binding