STX16-NPEPL1

STX16-NPEPL1 readthrough (NMD candidate)

Basic information

Region (hg38): 20:58651434-58715410

Links

ENSG00000254995 ∙ NCBI:100534593 ∙ ∙ HGNC:41993 ∙ ∙ ∙ 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 STX16-NPEPL1 gene.

• Pseudohypoparathyroidism type 1B (117 variants)
• not provided (64 variants)
• Inborn genetic diseases (35 variants)
• Autosomal dominant pseudohypoaldosteronism type 1 (8 variants)
• not specified (2 variants)
• STX16-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX16-NPEPL1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			3		2	5
splice region						0
non coding			102	26	70	198
Total	0	0	105	26	72

Variants in STX16-NPEPL1

This is a list of pathogenic ClinVar variants found in the STX16-NPEPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-58651457-G-A		Pseudohypoparathyroidism type 1B	Benign (Jan 13, 2018)
20-58651473-C-G		Pseudohypoparathyroidism type 1B	Benign (Jan 12, 2018)
20-58651513-G-A		Pseudohypoparathyroidism type 1B	Uncertain significance (Jan 12, 2018)
20-58651542-T-G		Pseudohypoparathyroidism type 1B	Uncertain significance (Jan 12, 2018)
20-58651543-G-A		Pseudohypoparathyroidism type 1B	Benign (Jul 01, 2022)
20-58651586-C-G		Pseudohypoparathyroidism type 1B	Benign (Jan 13, 2018)
20-58651598-G-A		Pseudohypoparathyroidism type 1B	Uncertain significance (Jan 12, 2018)
20-58651630-G-A		Pseudohypoparathyroidism type 1B	Uncertain significance (Jan 13, 2018)
20-58651652-C-T		Pseudohypoparathyroidism type 1B	Benign (Jan 13, 2018)
20-58651657-C-A		Pseudohypoparathyroidism type 1B	Benign (Jan 13, 2018)
20-58651847-G-A		Pseudohypoparathyroidism type 1B	Benign (Jan 13, 2018)
20-58651944-T-C		Pseudohypoparathyroidism type 1B	Benign (Jan 13, 2018)
20-58651982-A-C		Pseudohypoparathyroidism type 1B	Benign (Jan 13, 2018)
20-58652050-A-G		Inborn genetic diseases	Uncertain significance (May 25, 2022)
20-58652105-C-T			Likely benign (May 18, 2018)
20-58652106-T-TC			Uncertain significance (Jul 22, 2023)
20-58652112-C-A		Pseudohypoparathyroidism type 1B	Benign/Likely benign (Jun 19, 2022)
20-58652112-C-T		Inborn genetic diseases	Uncertain significance (Jan 22, 2024)
20-58652152-C-A			Likely benign (Jan 16, 2024)
20-58652153-G-A		Pseudohypoparathyroidism type 1B	Benign (Jan 04, 2024)
20-58652371-A-AC			Benign (May 26, 2021)
20-58659426-A-G			Benign (May 16, 2021)
20-58659457-AAAG-A			Benign (May 16, 2021)
20-58659605-G-A			Likely benign (Mar 19, 2022)
20-58659624-A-C		Inborn genetic diseases	Uncertain significance (May 03, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.515

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene ontology

• Biological process: intracellular protein transport;vesicle fusion;vesicle docking
• Cellular component: endomembrane system;integral component of membrane;SNARE complex
• Molecular function: SNARE binding;SNAP receptor activity