ESYT2

extended synaptotagmin 2, the group of Extended synaptotagmins

Basic information

Region (hg38): 7:158730995-158830253

Previous symbols: [ "FAM62B" ]

Links

ENSG00000117868 ∙ NCBI:57488 ∙ OMIM:616691 ∙ HGNC:22211 ∙ Uniprot:A0FGR8 ∙ 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 ESYT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESYT2 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			69	3		72
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	1		9
Total	0	0	77	4	0

Variants in ESYT2

This is a list of pathogenic ClinVar variants found in the ESYT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-158734224-G-A		not specified	Uncertain significance (Oct 20, 2024)
7-158734228-C-T			Likely benign (Mar 01, 2025)
7-158734447-C-T		not specified	Uncertain significance (Oct 27, 2023)
7-158735535-A-G		not specified	Uncertain significance (Jan 28, 2025)
7-158735538-C-T		not specified	Uncertain significance (May 21, 2024)
7-158735559-C-T		not specified	Uncertain significance (Oct 13, 2023)
7-158735562-C-A		not specified	Uncertain significance (Nov 15, 2021)
7-158735567-G-A		not specified	Uncertain significance (Aug 09, 2021)
7-158735591-G-A		not specified	Uncertain significance (Feb 23, 2023)
7-158737096-C-T		not specified	Uncertain significance (Jul 05, 2024)
7-158737141-T-C		not specified	Uncertain significance (Aug 17, 2021)
7-158739042-C-T		not specified	Uncertain significance (Dec 25, 2024)
7-158741548-G-A		not specified	Uncertain significance (Jul 09, 2024)
7-158741560-T-A		not specified	Uncertain significance (Apr 06, 2024)
7-158741566-T-C		not specified	Uncertain significance (Mar 03, 2025)
7-158741574-G-A		not specified	Uncertain significance (Apr 07, 2023)
7-158741604-T-C		not specified	Uncertain significance (Mar 01, 2024)
7-158741628-G-A		not specified	Uncertain significance (Feb 14, 2023)
7-158741659-G-C		not specified	Uncertain significance (Dec 01, 2024)
7-158741664-T-C		not specified	Likely benign (Jul 17, 2024)
7-158741667-A-T		not specified	Uncertain significance (Jun 01, 2023)
7-158741692-G-A		not specified	Uncertain significance (May 15, 2024)
7-158741733-A-G		not specified	Conflicting classifications of pathogenicity (Jan 03, 2024)
7-158741746-A-C		not specified	Uncertain significance (Jan 09, 2024)
7-158741778-G-T		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESYT2	protein_coding	protein_coding	ENST00000251527	22	99259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000779	1.00	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.551	421	454	0.927	0.0000250	5754
Missense in Polyphen		98	126.37	0.77551		1429
Synonymous	-0.448	190	182	1.04	0.0000106	1787
Loss of Function	3.87	17	45.1	0.377	0.00000229	546

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000331	0.000331
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.0000984	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane. Binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport. Plays a role in FGF signaling via its role in the rapid internalization of FGFR1 that has been activated by FGF1 binding; this occurs most likely via the AP-2 complex. {ECO:0000269|PubMed:17360437, ECO:0000269|PubMed:20833364, ECO:0000269|PubMed:23791178, ECO:0000269|PubMed:24847877}.
• Pathway: Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.522
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.61

Haploinsufficiency Scores

• pHI: 0.210
• hipred: N
• hipred_score: 0.476
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.909

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Esyt2
• Phenotype: immune system 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; cellular phenotype

Gene ontology

• Biological process: lipid transport;endocytosis;endoplasmic reticulum-plasma membrane tethering
• Cellular component: endoplasmic reticulum membrane;integral component of plasma membrane;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;identical protein binding;cadherin binding