SNX8

sorting nexin 8, the group of PX-BAR domain containing|Sorting nexins|MicroRNA protein coding host genes

Basic information

Region (hg38): 7:2251769-2354318

Links

ENSG00000106266 ∙ NCBI:29886 ∙ OMIM:614905 ∙ HGNC:14972 ∙ Uniprot:Q9Y5X2 ∙ 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 SNX8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX8 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	2
missense			35	1	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	35	2	4

Variants in SNX8

This is a list of pathogenic ClinVar variants found in the SNX8 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-2255073-C-T		not specified	Uncertain significance (Feb 26, 2024)
7-2255077-C-T			Likely benign (Feb 01, 2023)
7-2256858-A-G			Benign (Apr 14, 2019)
7-2256865-C-A			Benign (Sep 11, 2018)
7-2256896-G-A		not specified	Uncertain significance (Nov 17, 2022)
7-2256899-T-G		not specified	Uncertain significance (Jan 31, 2022)
7-2256953-T-A		not specified	Uncertain significance (Oct 04, 2022)
7-2256980-G-T		not specified	Uncertain significance (Oct 03, 2023)
7-2257402-G-A		not specified	Uncertain significance (Jan 23, 2024)
7-2257417-G-A		not specified	Likely benign (Sep 17, 2021)
7-2257418-C-A		not specified	Uncertain significance (Sep 17, 2021)
7-2257418-C-T		not specified	Uncertain significance (Sep 26, 2023)
7-2257434-C-G		not specified	Uncertain significance (May 06, 2024)
7-2257492-T-C		not specified	Uncertain significance (Jan 18, 2022)
7-2257502-G-A		not specified	Uncertain significance (Jun 17, 2024)
7-2257800-T-G		not specified	Uncertain significance (Jan 20, 2023)
7-2263247-C-T		not specified	Uncertain significance (Oct 04, 2022)
7-2263260-G-T		not specified	Uncertain significance (Oct 17, 2023)
7-2263321-G-C		not specified	Uncertain significance (Nov 13, 2023)
7-2263345-G-C		not specified	Uncertain significance (Mar 11, 2024)
7-2264329-C-T		not specified	Uncertain significance (Jul 08, 2022)
7-2264349-G-A		not specified	Uncertain significance (Jan 19, 2022)
7-2264352-G-A		not specified	Uncertain significance (Mar 20, 2024)
7-2264373-C-T		not specified	Uncertain significance (Nov 12, 2021)
7-2264433-G-A		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX8	protein_coding	protein_coding	ENST00000222990	11	102549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0624	0.937	125722	0	25	125747	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.282	262	275	0.952	0.0000182	3003
Missense in Polyphen		74	85.414	0.86637		911
Synonymous	-1.63	157	133	1.18	0.00000998	921
Loss of Function	3.00	6	20.8	0.289	9.49e-7	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000243
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000971	0.0000924
European (Non-Finnish)	0.000138	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in several stages of intracellular trafficking. May play a role in intracellular protein transport from early endosomes to the trans-Golgi network. {ECO:0000269|PubMed:19782049}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.147
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.51

Haploinsufficiency Scores

• pHI: 0.167
• hipred: Y
• hipred_score: 0.543
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.719

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx8

Gene ontology

• Biological process: intracellular protein transport;early endosome to Golgi transport
• Cellular component: cytosol;retromer complex;early endosome membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;phosphatidylinositol binding;identical protein binding