STX16

syntaxin 16, the group of Syntaxins

Basic information

Region (hg38): 20:58651272-58679526

Links

ENSG00000124222 ∙ NCBI:8675 ∙ OMIM:603666 ∙ HGNC:11431 ∙ Uniprot:O14662 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pseudohypoparathyroidism type 1B (Strong), mode of inheritance: AD
• pseudohypoparathyroidism type 1B (Supportive), mode of inheritance: AD
• pseudohypoparathyroidism type 1B (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Pseudohypoparathyroidism, type IB	AD	Endocrine; Renal	Complications such as osteitis fibrosa cystica may be effectively treated with calcium and vitamin D therapy	Endocrine; Renal	15537666; 17595244; 18626245; 20960161; 20538864; 21752878

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STX16 gene.

• Pseudohypoparathyroidism type 1B (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX16 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	14	3	19
missense			27	2	4	33
nonsense					1	1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2		2	4
non coding			60	12	60	132
Total	0	0	91	28	68

Variants in STX16

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

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

Position	Type	Phenotype	Significance	ClinVar
20-58651300-G-A		Pseudohypoparathyroidism type 1B	Uncertain significance (Jan 13, 2018)
20-58651314-G-A		Pseudohypoparathyroidism type 1B	Uncertain significance (Jan 13, 2018)
20-58651334-C-G		Pseudohypoparathyroidism type 1B	Uncertain significance (Jan 12, 2018)
20-58651386-G-A		Pseudohypoparathyroidism type 1B	Uncertain significance (Jan 13, 2018)
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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX16	protein_coding	protein_coding	ENST00000371141	9	28255

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.483	0.517	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.952	160	198	0.809	0.0000115	2126
Missense in Polyphen		35	46.14	0.75855		540
Synonymous	0.435	70	74.8	0.936	0.00000435	627
Loss of Function	3.19	4	19.0	0.210	0.00000102	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: SNARE involved in vesicular transport from the late endosomes to the trans-Golgi network. {ECO:0000269|PubMed:18195106}.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Ectoderm Differentiation;Vesicle-mediated transport;Membrane Trafficking;Intra-Golgi traffic;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.0823

Intolerance Scores

• loftool: 0.632
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.824
• hipred: N
• hipred_score: 0.462
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.863

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx16
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; normal phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Zebrafish Information Network

• Gene name: stx16
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: increased curvature

Gene ontology

• Biological process: intracellular protein transport;vesicle fusion;retrograde transport, endosome to Golgi;vesicle docking;Golgi ribbon formation
• Cellular component: Golgi membrane;cytoplasm;Golgi apparatus;trans-Golgi network;cytosol;focal adhesion;endomembrane system;integral component of membrane;SNARE complex;Golgi cisterna;trans-Golgi network membrane;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;syntaxin binding