ESYT3

extended synaptotagmin 3, the group of Extended synaptotagmins

Basic information

Region (hg38): 3:138434586-138481686

Previous symbols: [ "FAM62C" ]

Links

ENSG00000158220 ∙ NCBI:83850 ∙ OMIM:616692 ∙ HGNC:24295 ∙ Uniprot:A0FGR9 ∙ 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 ESYT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESYT3 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			77	4		81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	77	4	0

Variants in ESYT3

This is a list of pathogenic ClinVar variants found in the ESYT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-138434826-G-T		not specified	Uncertain significance (Jul 13, 2021)
3-138434865-C-A		not specified	Uncertain significance (Dec 21, 2022)
3-138435016-G-T		not specified	Uncertain significance (Jan 17, 2024)
3-138435109-A-T		not specified	Likely benign (Jan 29, 2024)
3-138452081-G-A		not specified	Uncertain significance (Nov 19, 2024)
3-138455201-C-T		not specified	Uncertain significance (Mar 01, 2023)
3-138455245-C-T		not specified	Uncertain significance (Oct 06, 2021)
3-138455266-A-G		not specified	Uncertain significance (Nov 07, 2024)
3-138455285-A-C		not specified	Uncertain significance (Feb 07, 2025)
3-138457569-G-A		not specified	Uncertain significance (Oct 25, 2023)
3-138457605-C-T		not specified	Uncertain significance (Mar 03, 2022)
3-138457620-G-T		not specified	Uncertain significance (Apr 19, 2024)
3-138457625-A-G		not specified	Uncertain significance (Feb 26, 2025)
3-138459234-C-A		not specified	Uncertain significance (Feb 05, 2025)
3-138459961-G-A		not specified	Uncertain significance (Jul 17, 2024)
3-138460020-T-G		not specified	Uncertain significance (Dec 23, 2024)
3-138460642-A-G		not specified	Uncertain significance (Jan 18, 2022)
3-138460643-C-A		not specified	Uncertain significance (Nov 18, 2023)
3-138460651-A-C		not specified	Uncertain significance (Nov 14, 2024)
3-138460654-C-T		not specified	Uncertain significance (Mar 23, 2023)
3-138462115-T-G		not specified	Uncertain significance (Apr 09, 2024)
3-138462123-A-G		not specified	Likely benign (Aug 10, 2021)
3-138462144-C-T		not specified	Uncertain significance (Dec 01, 2022)
3-138462186-C-A		not specified	Uncertain significance (Sep 03, 2024)
3-138462186-C-G		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESYT3	protein_coding	protein_coding	ENST00000389567	23	47101

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-25	0.00546	125494	0	254	125748	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0700	490	494	0.991	0.0000273	5707
Missense in Polyphen		161	184.16	0.87425		2179
Synonymous	0.922	187	204	0.918	0.0000109	1818
Loss of Function	0.927	42	49.0	0.857	0.00000269	537

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00283	0.00281
Ashkenazi Jewish	0.00	0.00
East Asian	0.00297	0.00294
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000682	0.000668
Middle Eastern	0.00297	0.00294
South Asian	0.00122	0.00114
Other	0.00167	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport (By similarity). Tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane. {ECO:0000250, ECO:0000269|PubMed:23791178}.
• Pathway: Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.561
• rvis_EVS: 1.9
• rvis_percentile_EVS: 97.34

Haploinsufficiency Scores

• pHI: 0.0727
• hipred: N
• hipred_score: 0.328
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.139

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Esyt3
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: lipid transport;endoplasmic reticulum-plasma membrane tethering
• Cellular component: endoplasmic reticulum membrane;integral component of plasma membrane;intrinsic component of endoplasmic reticulum membrane;extrinsic component of cytoplasmic side of plasma membrane;organelle membrane contact site;endoplasmic reticulum-plasma membrane contact site
• Molecular function: calcium ion binding;protein binding;calcium-dependent phospholipid binding;phosphatidylethanolamine binding;phosphatidylcholine binding;phosphatidylinositol binding