ECE2

endothelin converting enzyme 2, the group of M13 metallopeptidases

Basic information

Region (hg38): 3:184276010-184293031

Links

ENSG00000145194 ∙ NCBI:9718 ∙ OMIM:610145 ∙ HGNC:13275 ∙ Uniprot:P0DPD6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Alzheimer disease (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ECE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECE2 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				2	2	4
missense			46	3	1	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	5	3

Variants in ECE2

This is a list of pathogenic ClinVar variants found in the ECE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-184276980-C-T		not specified	Uncertain significance (Dec 02, 2022)
3-184276991-G-A		not specified	Uncertain significance (May 06, 2024)
3-184277016-A-G		not specified	Uncertain significance (Aug 02, 2023)
3-184277323-G-A		not specified	Uncertain significance (Jun 29, 2023)
3-184277340-G-A		not specified	Uncertain significance (Jan 31, 2022)
3-184277376-C-T		not specified	Uncertain significance (Dec 21, 2023)
3-184277377-G-A		not specified	Uncertain significance (Jan 22, 2024)
3-184277401-G-A		not specified	Uncertain significance (Oct 06, 2022)
3-184277961-A-G		not specified	Likely benign (Nov 07, 2022)
3-184277978-T-C		not specified	Uncertain significance (Jun 13, 2024)
3-184278191-C-T		not specified	Uncertain significance (Aug 12, 2021)
3-184278198-A-G		not specified	Uncertain significance (Aug 12, 2022)
3-184278213-T-C		not specified	Uncertain significance (Aug 12, 2021)
3-184278219-T-C		not specified	Uncertain significance (Aug 08, 2022)
3-184278245-A-T		not specified	Uncertain significance (Mar 12, 2024)
3-184278307-T-C			Benign (Jul 15, 2018)
3-184278551-T-A		not specified	Uncertain significance (Jul 12, 2022)
3-184283785-G-A		not specified	Uncertain significance (May 07, 2024)
3-184283840-G-A		not specified	Likely benign (Aug 12, 2022)
3-184283929-G-A		not specified	Uncertain significance (Dec 28, 2023)
3-184283963-C-T		not specified	Uncertain significance (Feb 06, 2023)
3-184285092-C-T		not specified	Uncertain significance (Mar 01, 2024)
3-184285096-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-184285529-C-T			Benign (Jun 20, 2018)
3-184287875-G-A			Likely benign (Apr 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECE2	protein_coding	protein_coding	ENST00000402825	19	43382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-21	0.111	125556	0	192	125748	0.000764

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.190	521	533	0.977	0.0000314	5764
Missense in Polyphen		258	272	0.94853		3014
Synonymous	-0.404	226	218	1.03	0.0000126	1738
Loss of Function	1.50	39	50.5	0.772	0.00000260	519

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00181	0.00180
Ashkenazi Jewish	0.000895	0.000893
East Asian	0.00126	0.00125
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000909	0.000888
Middle Eastern	0.00126	0.00125
South Asian	0.000509	0.000490
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts big endothelin-1 to endothelin-1. Also involved in the processing of various neuroendocrine peptides, including neurotensin, angiotensin I, substance P, proenkephalin-derived peptides, and prodynorphin-derived peptides. May play a role in amyloid-beta processing (By similarity). {ECO:0000250|UniProtKB:B2RQR8, ECO:0000269|PubMed:12560336}.
• Pathway: Signaling by GPCR;Signal Transduction;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding (Consensus)

Recessive Scores

• pRec: 0.0979

Intolerance Scores

• loftool: 0.0767
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.59

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.275
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.263

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ece2
• Phenotype: skeleton phenotype; hearing/vestibular/ear phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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; craniofacial phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: ece2b
• Affected structure: iridophore
• Phenotype tag: abnormal
• Phenotype quality: ridged

Gene ontology

• Biological process: peptide hormone processing;methylation
• Cellular component: Golgi membrane;integral component of membrane;transport vesicle membrane
• Molecular function: metalloendopeptidase activity;methyltransferase activity;metal ion binding