SNX19

sorting nexin 19, the group of Sorting nexins

Basic information

Region (hg38): 11:130866250-130916479

Links

ENSG00000120451 ∙ NCBI:399979 ∙ ∙ HGNC:21532 ∙ Uniprot:Q92543 ∙ 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 SNX19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX19 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				4		4
missense			60	5	3	68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	9	3

Variants in SNX19

This is a list of pathogenic ClinVar variants found in the SNX19 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-130878428-G-C			Likely benign (Mar 01, 2022)
11-130878526-T-C		not specified	Uncertain significance (Sep 16, 2021)
11-130878554-C-A		not specified	Uncertain significance (Nov 30, 2022)
11-130879634-G-C		not specified	Uncertain significance (Oct 12, 2021)
11-130879676-G-A		not specified	Uncertain significance (Dec 19, 2022)
11-130880687-C-A		not specified	Uncertain significance (Nov 14, 2023)
11-130880696-C-T		not specified	Uncertain significance (Oct 06, 2021)
11-130880697-G-A			Benign (Dec 31, 2019)
11-130880703-A-G		not specified	Uncertain significance (May 15, 2024)
11-130880720-C-T		not specified	Uncertain significance (Dec 19, 2022)
11-130880724-G-A		not specified	Uncertain significance (Dec 13, 2023)
11-130880756-T-C		not specified	Uncertain significance (Feb 28, 2024)
11-130903262-C-T		not specified	Likely benign (Nov 15, 2021)
11-130903304-C-T		not specified	Uncertain significance (Dec 15, 2023)
11-130903305-G-A			Likely benign (Nov 09, 2018)
11-130903310-A-G		not specified	Uncertain significance (Feb 15, 2023)
11-130903346-G-C			Likely benign (Dec 31, 2019)
11-130903366-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-130903384-C-G			Benign (Dec 31, 2019)
11-130905959-C-T		not specified	Uncertain significance (Aug 31, 2022)
11-130906001-C-A		not specified	Likely benign (Sep 22, 2023)
11-130906015-C-T		not specified	Likely benign (May 27, 2022)
11-130906632-C-T		not specified	Uncertain significance (Aug 30, 2021)
11-130907959-G-C		not specified	Uncertain significance (Mar 05, 2024)
11-130910112-G-A		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX19	protein_coding	protein_coding	ENST00000265909	11	41074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.83e-12	0.971	125610	0	138	125748	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.579	600	561	1.07	0.0000315	6386
Missense in Polyphen		155	164.84	0.94033		2025
Synonymous	-1.22	242	219	1.10	0.0000120	2099
Loss of Function	2.27	24	39.4	0.609	0.00000206	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000807	0.000806
Ashkenazi Jewish	0.00	0.00
East Asian	0.00114	0.00114
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000573	0.000571
Middle Eastern	0.00114	0.00114
South Asian	0.000728	0.000719
Other	0.000981	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in intracellular vesicle trafficking and exocytosis (PubMed:24843546). May play a role in maintaining insulin-containing dense core vesicles in pancreatic beta-cells and in preventing their degradation. May play a role in insulin secretion (PubMed:24843546). Interacts with membranes containing phosphatidylinositol 3-phosphate (PtdIns(3P)) (By similarity). {ECO:0000250|UniProtKB:Q6P4T1, ECO:0000269|PubMed:24843546}.

Recessive Scores

• pRec: 0.0973

Intolerance Scores

• loftool: 0.963
• rvis_EVS: 1.37
• rvis_percentile_EVS: 94.46

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.368
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx19

Gene ontology

• Biological process: chondrocyte differentiation;exocytosis;insulin secretion;dense core granule maturation
• Cellular component: cytoplasm;cytoplasmic vesicle membrane;early endosome membrane
• Molecular function: protein binding;phosphatidylinositol-3-phosphate binding