SNX13

sorting nexin 13, the group of Sorting nexins

Basic information

Region (hg38): 7:17790761-17940501

Links

ENSG00000071189 ∙ NCBI:23161 ∙ OMIM:606589 ∙ HGNC:21335 ∙ Uniprot:Q9Y5W8 ∙ 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 SNX13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX13 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				2	1	3
missense			47	1		48
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	47	3	3

Variants in SNX13

This is a list of pathogenic ClinVar variants found in the SNX13 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-17794079-T-G		not specified	Uncertain significance (Aug 17, 2021)
7-17794102-C-T		not specified	Uncertain significance (Jul 11, 2022)
7-17794131-T-C		not specified	Uncertain significance (Aug 21, 2023)
7-17794143-G-A		not specified	Uncertain significance (May 18, 2022)
7-17794179-C-T		not specified	Uncertain significance (Feb 28, 2024)
7-17794188-A-G		not specified	Uncertain significance (Jan 16, 2024)
7-17794274-A-G		not specified	Uncertain significance (Feb 26, 2024)
7-17796877-C-T		not specified	Uncertain significance (Mar 27, 2023)
7-17796881-T-A		not specified	Uncertain significance (Jul 26, 2021)
7-17801593-C-T		not specified	Uncertain significance (Jun 21, 2022)
7-17801638-T-C		not specified	Uncertain significance (Jun 29, 2023)
7-17801646-A-G		not specified	Uncertain significance (Oct 27, 2022)
7-17803507-C-T		not specified	Uncertain significance (Feb 28, 2024)
7-17803526-C-A		not specified	Uncertain significance (Jan 26, 2022)
7-17803540-T-G		not specified	Uncertain significance (Aug 05, 2023)
7-17814916-G-A		not specified	Uncertain significance (Dec 21, 2023)
7-17814952-G-GAA		not specified	Benign (Mar 29, 2016)
7-17816247-T-C		not specified	Uncertain significance (Jul 19, 2023)
7-17821556-G-A		not specified	Uncertain significance (Nov 22, 2022)
7-17821592-G-A		not specified	Uncertain significance (Dec 26, 2023)
7-17821597-T-A		not specified	Uncertain significance (Mar 20, 2023)
7-17821635-A-T		not specified	Uncertain significance (Nov 08, 2022)
7-17830016-T-C		not specified	Uncertain significance (Apr 16, 2024)
7-17834069-G-A		not specified	Uncertain significance (Apr 09, 2024)
7-17834118-G-A		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX13	protein_coding	protein_coding	ENST00000428135	26	149740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.403	0.597	124607	0	16	124623	0.0000642

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	336	455	0.738	0.0000235	6257
Missense in Polyphen		73	135.99	0.53682		1885
Synonymous	-1.56	173	149	1.16	0.00000723	1684
Loss of Function	5.25	12	53.4	0.225	0.00000283	734

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000141	0.000139
European (Non-Finnish)	0.0000830	0.0000796
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in several stages of intracellular trafficking. May play a role in endosome homeostasis (By similarity). Acts as a GAP for Galphas. {ECO:0000250, ECO:0000269|PubMed:11729322}.

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.523
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.567
• hipred: Y
• hipred_score: 0.575
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx13
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: snx13
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: apoptotic

Gene ontology

• Biological process: intracellular protein transport;negative regulation of signal transduction;positive regulation of GTPase activity
• Cellular component: early endosome;early endosome membrane
• Molecular function: phosphatidylinositol-3-phosphate binding;phosphatidylinositol binding