ESYT2

protein-coding

extended synaptotagmin 2, the group of Extended synaptotagmins

Gene summary

Enables several functions, including identical protein binding activity; phosphatidylinositol binding activity; and phospholipid binding activity. Predicted to be involved in endocytosis; endoplasmic reticulum-plasma membrane tethering; and lipid transport. Located in cytoplasmic side of plasma membrane; endoplasmic reticulum membrane; and endoplasmic reticulum-plasma membrane contact site. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM62B

MANE transcript

NM_001367773.1

Inheritance

—

ClinVar variants

U:148B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr7:158,730,995-158,830,253

External References & Databases

Ensembl (ENSG00000117868)

Transcript & Mutation Effects

hg38 • Region Span ~99.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ESYT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 138

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001367773.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			139 clinvar	4 clinvar		143
nonsense			1 clinvar			1
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	148	6	0	154

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 75 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001367773.1	RefSeq	NP_001354702.1	23	MANE Select
ENST00000275418.13	Ensembl	ENSP00000275418.8	23	MANE Select
NM_020728.3	RefSeq	NP_065779.2	22	Standard
ENST00000251527.10	Ensembl	ENSP00000251527.6	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Metabolism
Glycosphingolipid metabolism
Sphingolipid metabolism

Biological Process

lipid transport
endocytosis
endoplasmic reticulum-plasma membrane tethering

Molecular Function

calcium ion binding
protein binding
calcium-dependent phospholipid binding
phosphatidylethanolamine binding
phosphatidylcholine binding

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000251527
Coding exons: 22
Length: 99259
Individuals with no LoFs: 125710
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 125748
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.551	421	454	0.927	0.0000250	5754
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.000098	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.522
RVIS EVS: -0.11
RVIS percentile EVS: 45.61

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.909

Gene Damage Prediction

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