ESYT1

extended synaptotagmin 1, the group of Extended synaptotagmins

Basic information

Region (hg38): 12:56118250-56144674

Previous symbols: [ "FAM62A" ]

Links

ENSG00000139641 ∙ NCBI:23344 ∙ OMIM:616670 ∙ HGNC:29534 ∙ Uniprot:Q9BSJ8 ∙ 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 ESYT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESYT1 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					4	4
missense			75	2		77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	75	2	4

Variants in ESYT1

This is a list of pathogenic ClinVar variants found in the ESYT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-56120627-G-A		not specified	Uncertain significance (Jul 09, 2024)
12-56120632-G-A		not specified	Uncertain significance (Dec 10, 2024)
12-56120634-G-T		not specified	Uncertain significance (Jun 28, 2022)
12-56120726-G-A		not specified	Uncertain significance (Apr 15, 2024)
12-56120791-A-G		not specified	Uncertain significance (Apr 18, 2023)
12-56120873-G-T		not specified	Uncertain significance (Aug 01, 2024)
12-56120983-C-T		not specified	Uncertain significance (Jul 20, 2022)
12-56121070-G-C		not specified	Uncertain significance (Dec 01, 2022)
12-56121077-G-T		not specified	Uncertain significance (Dec 17, 2023)
12-56121092-C-T		not specified	Uncertain significance (Jul 25, 2023)
12-56121094-A-G		not specified	Uncertain significance (Jul 15, 2024)
12-56121110-C-CAGGACGACGTCATGATCTCTATGAT			Uncertain significance (Jul 01, 2019)
12-56121118-C-T		not specified	Uncertain significance (Jun 25, 2024)
12-56121131-A-G		not specified	Uncertain significance (Sep 27, 2024)
12-56121143-A-C		not specified	Uncertain significance (Jul 09, 2024)
12-56121146-T-A		not specified	Uncertain significance (Mar 11, 2024)
12-56121187-C-T			Uncertain significance (Jul 01, 2019)
12-56121211-C-G		not specified	Uncertain significance (Dec 19, 2022)
12-56121211-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-56121233-C-T		not specified	Uncertain significance (Oct 10, 2023)
12-56121257-C-T		not specified	Uncertain significance (Jun 23, 2023)
12-56121260-G-A		not specified	Uncertain significance (Mar 30, 2024)
12-56121532-C-T		not specified	Uncertain significance (Aug 02, 2023)
12-56121583-C-T		not specified	Uncertain significance (Jun 26, 2023)
12-56121640-C-G		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESYT1	protein_coding	protein_coding	ENST00000541590	31	26422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-13	1.00	125601	1	146	125748	0.000585

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.846	568	628	0.905	0.0000358	7145
Missense in Polyphen		179	224.1	0.79876		2577
Synonymous	1.88	210	248	0.848	0.0000129	2315
Loss of Function	4.21	34	72.8	0.467	0.00000425	748

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000514	0.000514
Ashkenazi Jewish	0.00397	0.00388
East Asian	0.000326	0.000326
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000555	0.000554
Middle Eastern	0.000326	0.000326
South Asian	0.000622	0.000621
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport (By similarity). Binds calcium (via the C2 domains) and translocates to sites of contact between the endoplasmic reticulum and the cell membrane in response to increased cytosolic calcium levels. Helps tether 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, ECO:0000269|PubMed:24183667}.
• Pathway: Metabolism of lipids;Metabolism;EGFR1;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.930
• rvis_EVS: -1.86
• rvis_percentile_EVS: 2.02

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.428
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.354

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Esyt1
• Phenotype: normal phenotype

Gene ontology

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