SYTL4

synaptotagmin like 4, the group of Synaptotagmin like tandem C2 proteins

Basic information

Region (hg38): X:100671783-100732123

Links

ENSG00000102362 ∙ NCBI:94121 ∙ OMIM:300723 ∙ HGNC:15588 ∙ Uniprot:Q96C24 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinal disorder (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYTL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYTL4 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				1		1
missense			35	2		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	35	3	0

Variants in SYTL4

This is a list of pathogenic ClinVar variants found in the SYTL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-100676045-G-T		not specified	Uncertain significance (Dec 01, 2022)
X-100676068-T-G		not specified	Uncertain significance (Feb 07, 2023)
X-100676079-T-C			Likely benign (Jan 01, 2023)
X-100676113-T-A		not specified	Uncertain significance (Sep 02, 2024)
X-100678480-T-C		not specified	Uncertain significance (Sep 10, 2024)
X-100678543-T-C		not specified	Uncertain significance (Jun 19, 2024)
X-100678561-T-G		not specified	Uncertain significance (Nov 25, 2024)
X-100678565-G-A		not specified	Uncertain significance (May 07, 2024)
X-100678577-T-C		not specified	Uncertain significance (Nov 29, 2024)
X-100678589-G-A		not specified	Uncertain significance (Nov 26, 2024)
X-100679355-G-A		not specified	Uncertain significance (Apr 25, 2023)
X-100679356-T-A		not specified	Uncertain significance (Apr 11, 2023)
X-100679401-C-T			Likely benign (Mar 01, 2023)
X-100681236-G-A		not specified	Uncertain significance (Dec 13, 2024)
X-100681308-G-A		not specified	Uncertain significance (Apr 04, 2024)
X-100681319-G-A		not specified	Likely benign (Aug 20, 2023)
X-100681326-C-T		not specified	Uncertain significance (May 16, 2023)
X-100685997-T-C		not specified	Uncertain significance (Feb 07, 2025)
X-100686074-G-C		not specified	Uncertain significance (Nov 23, 2024)
X-100686087-C-T		not specified	Uncertain significance (Feb 14, 2025)
X-100686088-G-A		not specified	Uncertain significance (Oct 27, 2022)
X-100686110-C-A		not specified	Uncertain significance (Feb 25, 2025)
X-100686155-T-C			Likely benign (Nov 01, 2022)
X-100686686-G-A		not specified	Uncertain significance (Jan 03, 2025)
X-100686747-G-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYTL4	protein_coding	protein_coding	ENST00000455616	16	57623

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0141	0.986	125701	10	26	125737	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.812	222	259	0.858	0.0000204	4430
Missense in Polyphen		70	94.865	0.73789		1587
Synonymous	2.15	65	91.1	0.713	0.00000661	1255
Loss of Function	3.21	8	25.5	0.314	0.00000191	444

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000528	0.000528
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000223	0.000149
Middle Eastern	0.00	0.00
South Asian	0.0000597	0.0000327
Other	0.000955	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates exocytosis of dense-core granules and secretion of hormones in the pancreas and the pituitary. Interacts with vesicles containing negatively charged phospholipids in a Ca(2+)-independent manner (By similarity). {ECO:0000250}.
• Pathway: Deregulation of Rab and Rab Effector Genes in Bladder Cancer;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.729
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.304
• hipred: Y
• hipred_score: 0.726
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.524

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sytl4
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: platelet degranulation;intracellular protein transport;positive regulation of exocytosis;negative regulation of insulin secretion;positive regulation of protein secretion;multivesicular body sorting pathway
• Cellular component: nucleoplasm;endosome;microtubule organizing center;cytosol;plasma membrane;extrinsic component of membrane;transport vesicle membrane;platelet alpha granule membrane;exocytic vesicle
• Molecular function: protein binding;phospholipid binding;Rab GTPase binding;neurexin family protein binding;metal ion binding