SYT12

synaptotagmin 12, the group of MicroRNA protein coding host genes|Synaptotagmins

Basic information

Region (hg38): 11:67006778-67050863

Links

ENSG00000173227 ∙ NCBI:91683 ∙ OMIM:606436 ∙ HGNC:18381 ∙ Uniprot:Q8IV01 ∙ 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 SYT12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT12 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			45	1		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	1	0

Variants in SYT12

This is a list of pathogenic ClinVar variants found in the SYT12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67030161-C-T		not specified	Uncertain significance (Jun 22, 2023)
11-67030163-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-67034681-A-G		not specified	Uncertain significance (Feb 19, 2025)
11-67034686-G-T		not specified	Uncertain significance (Aug 28, 2023)
11-67034687-C-T		not specified	Uncertain significance (Dec 16, 2021)
11-67034699-C-G		not specified	Uncertain significance (Jan 05, 2022)
11-67034768-C-T		not specified	Uncertain significance (Oct 05, 2021)
11-67039820-G-T		not specified	Uncertain significance (Aug 12, 2024)
11-67039863-G-A		not specified	Uncertain significance (Mar 19, 2024)
11-67039890-C-T		not specified	Uncertain significance (May 10, 2023)
11-67039934-C-G		not specified	Uncertain significance (Mar 03, 2025)
11-67039942-G-T		not specified	Uncertain significance (Oct 25, 2023)
11-67039967-C-T		not specified	Uncertain significance (Oct 14, 2021)
11-67039968-G-A		not specified	Uncertain significance (Sep 11, 2024)
11-67040018-A-G		not specified	Uncertain significance (Jan 20, 2025)
11-67040093-G-A		not specified	Uncertain significance (Mar 20, 2024)
11-67040097-C-T		not specified	Uncertain significance (Oct 03, 2022)
11-67040126-C-T		not specified	Uncertain significance (Aug 12, 2021)
11-67040127-G-A		not specified	Likely benign (Oct 26, 2021)
11-67040129-G-A		not specified	Uncertain significance (Oct 26, 2024)
11-67040144-G-A		not specified	Uncertain significance (Nov 13, 2024)
11-67040159-C-T		not specified	Uncertain significance (Dec 07, 2021)
11-67040175-C-T		not specified	Uncertain significance (Apr 06, 2024)
11-67040201-C-T		not specified	Uncertain significance (Nov 18, 2023)
11-67043653-T-C		not specified	Uncertain significance (Feb 12, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT12	protein_coding	protein_coding	ENST00000393946	7	44086

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000174	0.888	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.307	264	278	0.948	0.0000184	2753
Missense in Polyphen		73	75.38	0.96842		731
Synonymous	0.318	119	124	0.964	0.00000896	860
Loss of Function	1.51	10	16.7	0.600	7.14e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000279	0.000274
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000201	0.000193
Middle Eastern	0.00	0.00
South Asian	0.000268	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis. {ECO:0000250}.
• Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Intolerance Scores

• loftool: 0.816
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.15

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.300
• ghis: 0.647

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.394

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt12

Gene ontology

• Biological process: regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;regulation of neurotransmitter secretion;spontaneous exocytosis of neurotransmitter;long-term synaptic potentiation;cellular response to calcium ion
• Cellular component: plasma membrane;integral component of membrane;cell junction;synaptic vesicle membrane;exocytic vesicle
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;calcium-dependent phospholipid binding;clathrin binding