NCEH1

neutral cholesterol ester hydrolase 1, the group of Arylacetamide deacetylase family

Basic information

Region (hg38): 3:172630248-172711218

Previous symbols: [ "AADACL1" ]

Links

ENSG00000144959 ∙ NCBI:57552 ∙ OMIM:613234 ∙ HGNC:29260 ∙ Uniprot:Q6PIU2 ∙ 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 NCEH1 gene.

• Inborn genetic diseases (18 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCEH1 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					1	1
missense			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	17	1	2

Variants in NCEH1

This is a list of pathogenic ClinVar variants found in the NCEH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-172633518-C-T		not specified	Uncertain significance (Mar 17, 2023)
3-172633536-T-C		not specified	Uncertain significance (Aug 12, 2022)
3-172633600-C-T		not specified	Uncertain significance (Aug 15, 2023)
3-172633623-C-T		not specified	Uncertain significance (Feb 09, 2023)
3-172633735-G-A		not specified	Uncertain significance (Jul 08, 2022)
3-172633761-T-C		not specified	Uncertain significance (Dec 05, 2022)
3-172633768-T-C		not specified	Uncertain significance (Jan 02, 2024)
3-172633848-C-T		not specified	Uncertain significance (Jun 21, 2022)
3-172633900-C-T		not specified	Likely benign (Jun 03, 2022)
3-172633926-T-C		not specified	Uncertain significance (Jul 12, 2022)
3-172633963-C-T		not specified	Uncertain significance (Jul 21, 2021)
3-172633969-G-A		not specified	Uncertain significance (Nov 08, 2021)
3-172635992-T-C		not specified	Uncertain significance (Feb 23, 2023)
3-172645678-C-G		not specified	Uncertain significance (May 25, 2022)
3-172647931-T-C		not specified	Uncertain significance (Jun 06, 2023)
3-172647949-C-T		not specified	Uncertain significance (Jun 16, 2023)
3-172648004-G-A			Benign (Jul 26, 2018)
3-172648098-T-C		not specified	Uncertain significance (Dec 28, 2022)
3-172710939-C-T			Benign (Feb 26, 2019)
3-172710956-G-A		not specified	Uncertain significance (Dec 15, 2023)
3-172711013-T-C		not specified	Uncertain significance (Apr 06, 2022)
3-172711050-C-G		not specified	Uncertain significance (Jan 10, 2023)
3-172711074-T-G		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCEH1	protein_coding	protein_coding	ENST00000538775	5	80970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0130	0.981	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.669	226	256	0.882	0.0000136	2909
Missense in Polyphen		55	93.929	0.58555		1110
Synonymous	0.176	104	106	0.978	0.00000592	930
Loss of Function	2.39	6	16.4	0.365	6.96e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000904
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000223	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.000327	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes 2-acetyl monoalkylglycerol ether, the penultimate precursor of the pathway for de novo synthesis of platelet-activating factor. May be responsible for cholesterol ester hydrolysis in macrophages, thereby contributing to the development of atherosclerosis. Also involved in organ detoxification by hydrolyzing exogenous organophosphorus compounds. May contribute to cancer pathogenesis by promoting tumor cell migration. {ECO:0000269|PubMed:17052608}.
• Pathway: Cortisol synthesis and secretion - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Bile secretion - Homo sapiens (human);Cholesterol metabolism - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;LDL clearance;Plasma lipoprotein clearance;Transport of small molecules;Plasma lipoprotein assembly, remodeling, and clearance (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.738
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.261
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nceh1
• Phenotype: homeostasis/metabolism phenotype; cellular 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); hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: lipid catabolic process;low-density lipoprotein particle clearance
• Cellular component: endoplasmic reticulum membrane;membrane;integral component of membrane
• Molecular function: sterol esterase activity