SYT16

synaptotagmin 16, the group of Synaptotagmins

Basic information

Region (hg38): 14:61811974-62112550

Previous symbols: [ "SYT14L" ]

Links

ENSG00000139973 ∙ NCBI:83851 ∙ OMIM:610950 ∙ HGNC:23142 ∙ Uniprot:Q17RD7 ∙ 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 SYT16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT16 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			36	3		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	0

Variants in SYT16

This is a list of pathogenic ClinVar variants found in the SYT16 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-61996113-G-A		not specified	Uncertain significance (Feb 27, 2023)
14-61996117-A-G		not specified	Uncertain significance (Mar 30, 2024)
14-61996148-C-G		not specified	Uncertain significance (Oct 12, 2021)
14-61996248-A-G		not specified	Uncertain significance (Jun 22, 2024)
14-61996251-C-G		not specified	Uncertain significance (Jun 01, 2023)
14-61996263-A-C		not specified	Uncertain significance (Mar 02, 2023)
14-61996363-A-G		not specified	Uncertain significance (May 30, 2023)
14-61996393-A-G		not specified	Likely benign (Jan 23, 2024)
14-61996437-A-C		not specified	Uncertain significance (Apr 18, 2023)
14-61996515-T-G		not specified	Uncertain significance (Aug 21, 2023)
14-61996539-C-A		not specified	Uncertain significance (Nov 13, 2023)
14-62069632-T-G		not specified	Uncertain significance (Feb 28, 2023)
14-62069662-A-G		not specified	Uncertain significance (Sep 06, 2022)
14-62069690-G-A		not specified	Uncertain significance (Dec 06, 2022)
14-62069705-G-A		not specified	Uncertain significance (Nov 06, 2023)
14-62069765-G-A		not specified	Likely benign (Jan 26, 2022)
14-62075155-C-T		not specified	Uncertain significance (May 27, 2022)
14-62075158-C-T		not specified	Uncertain significance (Feb 15, 2023)
14-62075159-G-A		not specified	Uncertain significance (Dec 16, 2021)
14-62075180-A-G		not specified	Uncertain significance (Dec 14, 2023)
14-62075198-T-C		not specified	Uncertain significance (May 01, 2022)
14-62075203-G-C		not specified	Uncertain significance (May 17, 2023)
14-62075221-T-C		not specified	Uncertain significance (Oct 05, 2023)
14-62075225-A-G		not specified	Uncertain significance (Aug 13, 2021)
14-62075290-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT16	protein_coding	protein_coding	ENST00000430451	6	114629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000202	0.995	124630	0	26	124656	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.197	381	370	1.03	0.0000213	4265
Missense in Polyphen		69	89.812	0.76827		974
Synonymous	-0.0763	147	146	1.01	0.00000880	1229
Loss of Function	2.48	14	28.2	0.496	0.00000172	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000301	0.000291
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000127	0.000111
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.000106	0.0000973
Middle Eastern	0.000127	0.000111
South Asian	0.0000654	0.0000654
Other	0.000356	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues. Is Ca(2+)-independent.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.672
• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.8

Haploinsufficiency Scores

• pHI: 0.274
• hipred: N
• hipred_score: 0.309

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00211

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt16

Gene ontology

• Biological process: exocytosis
• Molecular function: protein binding;phospholipid binding;protein homodimerization activity;protein heterodimerization activity