SYT13

synaptotagmin 13, the group of Synaptotagmins

Basic information

Region (hg38): 11:45240301-45286341

Links

ENSG00000019505 ∙ NCBI:57586 ∙ OMIM:607716 ∙ HGNC:14962 ∙ Uniprot:Q7L8C5 ∙ 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 SYT13 gene.

• Inborn genetic diseases (17 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT13 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	2
missense			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	2

Variants in SYT13

This is a list of pathogenic ClinVar variants found in the SYT13 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-45244134-G-A		not specified	Uncertain significance (Sep 29, 2022)
11-45244140-T-A		not specified	Uncertain significance (Nov 17, 2022)
11-45244256-C-G		not specified	Uncertain significance (Dec 13, 2022)
11-45246505-G-C		not specified	Uncertain significance (Mar 11, 2024)
11-45246508-G-T		not specified	Uncertain significance (May 24, 2023)
11-45252453-C-A		not specified	Uncertain significance (Feb 21, 2024)
11-45252467-A-G		not specified	Uncertain significance (Jan 09, 2024)
11-45252480-C-A		not specified	Uncertain significance (Mar 17, 2023)
11-45252481-C-T			Benign (Nov 19, 2018)
11-45252491-C-T		not specified	Uncertain significance (Nov 21, 2022)
11-45252548-G-A		not specified	Uncertain significance (Oct 04, 2022)
11-45252623-C-G		not specified	Uncertain significance (Aug 10, 2023)
11-45252661-C-A		not specified	Uncertain significance (Oct 29, 2021)
11-45254287-A-G		not specified	Uncertain significance (May 05, 2023)
11-45254315-C-T		not specified	Uncertain significance (May 25, 2022)
11-45254343-G-A			Benign (Nov 19, 2018)
11-45254387-A-T		not specified	Uncertain significance (Aug 10, 2023)
11-45255704-C-A		not specified	Uncertain significance (Aug 17, 2022)
11-45255714-G-C		not specified	Uncertain significance (Jan 06, 2023)
11-45255806-G-A		not specified	Uncertain significance (Nov 03, 2022)
11-45255864-C-G		not specified	Uncertain significance (Jun 30, 2022)
11-45255872-G-A		not specified	Uncertain significance (Dec 22, 2023)
11-45255884-A-C		not specified	Uncertain significance (Aug 12, 2021)
11-45286039-C-G		not specified	Likely benign (Aug 12, 2021)
11-45286105-G-T		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT13	protein_coding	protein_coding	ENST00000020926	6	46019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.688	0.312	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.363	237	253	0.936	0.0000141	2736
Missense in Polyphen		83	90.87	0.9134		986
Synonymous	0.123	111	113	0.985	0.00000647	902
Loss of Function	3.13	3	16.9	0.178	8.17e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000909	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000538	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transport vesicle docking to the plasma membrane. {ECO:0000250}.

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.413
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.737
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt13

Zebrafish Information Network

• Gene name: syt13
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;cellular response to calcium ion
• Cellular component: plasma membrane;integral component of plasma membrane;transport vesicle;intracellular membrane-bounded organelle;exocytic vesicle;presynapse
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;calcium-dependent phospholipid binding;syntaxin binding;clathrin binding