SNX11

sorting nexin 11, the group of Sorting nexins

Basic information

Region (hg38): 17:48103357-48123601

Links

ENSG00000002919 ∙ NCBI:29916 ∙ OMIM:614906 ∙ HGNC:14975 ∙ Uniprot:Q9Y5W9 ∙ 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 SNX11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX11 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			17	1		18
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	17	1	0

Variants in SNX11

This is a list of pathogenic ClinVar variants found in the SNX11 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48112605-G-A		not specified	Uncertain significance (Aug 01, 2024)
17-48113305-A-G		not specified	Uncertain significance (Jul 16, 2024)
17-48113347-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-48113353-G-A		not specified	Uncertain significance (Sep 08, 2024)
17-48118704-G-A		not specified	Likely benign (Jan 23, 2024)
17-48118774-C-G		not specified	Uncertain significance (Oct 03, 2022)
17-48118784-A-G		not specified	Uncertain significance (Dec 13, 2024)
17-48118792-C-T		not specified	Uncertain significance (May 05, 2023)
17-48118974-G-C		not specified	Uncertain significance (Jan 24, 2023)
17-48119002-G-C		not specified	Uncertain significance (Feb 13, 2024)
17-48119026-C-A		not specified	Uncertain significance (May 05, 2022)
17-48119105-G-A		not specified	Uncertain significance (Nov 15, 2024)
17-48121279-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-48121311-G-C		not specified	Uncertain significance (Nov 11, 2024)
17-48121339-T-C		not specified	Likely benign (May 17, 2023)
17-48121374-T-C		not specified	Uncertain significance (Jan 09, 2025)
17-48121380-C-T		not specified	Uncertain significance (Nov 08, 2021)
17-48121417-C-G		not specified	Uncertain significance (Mar 05, 2025)
17-48121443-G-C		not specified	Uncertain significance (Sep 25, 2024)
17-48121453-G-A		not specified	Uncertain significance (Sep 16, 2021)
17-48121464-G-A		not specified	Uncertain significance (Oct 20, 2021)
17-48121497-T-G		not specified	Uncertain significance (Jul 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX11	protein_coding	protein_coding	ENST00000393405	6	19718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.30e-7	0.730	125710	0	37	125747	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.724	124	149	0.833	0.00000816	1745
Missense in Polyphen		47	61.465	0.76466		689
Synonymous	0.843	47	55.0	0.855	0.00000287	543
Loss of Function	1.22	12	17.5	0.685	0.00000117	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000322	0.000322
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000217	0.000217
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphoinositide-binding protein involved in protein sorting and membrane trafficking in endosomes. {ECO:0000269|PubMed:23615901}.

Intolerance Scores

• loftool: 0.920
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.0918
• hipred: N
• hipred_score: 0.244
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0191

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx11

Gene ontology

• Biological process: intracellular protein transport;vesicle organization
• Cellular component: endosome;membrane
• Molecular function: protein binding;phosphatidylinositol phosphate binding