SNX19

protein-coding

sorting nexin 19, the group of Sorting nexins

Gene summary

Islet antigen-2 (IA-2) is an autoantigen in type 1 diabetes and plays a role in insulin secretion. IA-2 is found in dense-core secretory vesicles and interacts with the product of this gene, a sorting nexin. In mouse pancreatic beta-cells, the encoded protein influenced insulin secretion by stabilizing the number of dense-core secretory vesicles. [provided by RefSeq, Dec 2016]

MANE transcript

NM_014758.3

Inheritance

—

ClinVar variants

U:153B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr11:130,866,250-130,916,479

External References & Databases

Ensembl (ENSG00000120451)

Transcript & Mutation Effects

hg38 • Region Span ~50.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SNX19 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 152

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014758.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	4 clinvar		6
missense			148 clinvar	8 clinvar	3 clinvar	159
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	153	12	3	168

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014758.3	RefSeq	NP_055573.3	11	MANE Select
ENST00000265909.9	Ensembl	ENSP00000265909.4	11	MANE Select
NM_001301089.2	RefSeq	NP_001288018.1	9	Standard
NM_001347918.2	RefSeq	NP_001334847.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

chondrocyte differentiation
exocytosis
insulin secretion
dense core granule maturation

Molecular Function

protein binding
phosphatidylinositol-3-phosphate binding

Cellular Component

cytoplasm
cytoplasmic vesicle membrane
early endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265909
Coding exons: 11
Length: 41074
Individuals with no LoFs: 125610
Homozygous LoFs: 0
Heterozygous LoFs: 138
Defined: 125748
p: 0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.579	600	561	1.07	0.0000315	6386
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00044	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0011	0.0011	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00057	0.00057	rare
South Asian	0.00073	0.00072	rare
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.119

Gene Damage Prediction

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