APOO

apolipoprotein O, the group of Mitochondrial contact site and cristae organizing system subunits|Apolipoproteins

Basic information

Region (hg38): X:23833353-23907938

Previous symbols: [ "FAM121B" ]

Links

ENSG00000184831 ∙ NCBI:79135 ∙ OMIM:300753 ∙ HGNC:28727 ∙ Uniprot:Q9BUR5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial disease (Limited), mode of inheritance: XL

ClinVar

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

• Cognitive impairment and autistic features;X-­linked recessive mitochondrial myopathy;Lactic acidosis (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOO 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	1		7		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	1	0	7	1	2

Variants in APOO

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

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

Position	Type	Phenotype	Significance	ClinVar
X-23856343-A-G		not specified	Uncertain significance (Jul 26, 2024)
X-23856367-A-C			Benign (Feb 25, 2018)
X-23856375-C-G		not specified	Uncertain significance (Jul 15, 2021)
X-23856377-A-G		APOO-related disorder	Likely benign (Jul 14, 2021)
X-23858679-G-T		not specified	Uncertain significance (Dec 25, 2024)
X-23858716-G-T		not specified	Uncertain significance (Nov 08, 2024)
X-23868631-A-G		Lactic acidosis;Cognitive impairment and autistic features;X-­linked recessive mitochondrial myopathy	Pathogenic (Mar 25, 2020)
X-23868676-T-C		not specified	Uncertain significance (Jan 23, 2025)
X-23868687-G-C		not specified	Uncertain significance (Aug 25, 2024)
X-23878928-G-T		not specified	Uncertain significance (Jul 12, 2022)
X-23878929-T-A		not specified	Uncertain significance (Dec 31, 2024)
X-23879005-T-C			Likely benign (Mar 01, 2022)
X-23879019-C-A		not specified	Uncertain significance (Oct 28, 2024)
X-23880829-A-G			Benign (Apr 29, 2019)
X-23880859-C-T		not specified	Conflicting classifications of pathogenicity (Feb 05, 2024)
X-23880886-T-C		not specified	Uncertain significance (Dec 11, 2024)
X-23880889-G-C		not specified	Uncertain significance (Feb 21, 2025)
X-23880906-A-G		not specified	Uncertain significance (Dec 30, 2024)
X-23880919-T-A		APOO-related disorder	Likely benign (May 18, 2023)
X-23880937-C-G		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOO	protein_coding	protein_coding	ENST00000379226	8	74588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.602	0.396	125439	4	2	125445	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0406	70	69.1	1.01	0.00000506	1259
Missense in Polyphen		27	20.039	1.3473		417
Synonymous	-0.233	29	27.4	1.06	0.00000229	366
Loss of Function	2.59	2	11.5	0.174	8.83e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000140	0.0000994
East Asian	0.00	0.00
Finnish	0.000193	0.000139
European (Non-Finnish)	0.0000128	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000531	0.0000329
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Plays a crucial role in crista junction formation and mitochondrial function (PubMed:25764979). Can promote cardiac lipotoxicity by enhancing mitochondrial respiration and fatty acid metabolism in cardiac myoblasts (PubMed:24743151). Promotes cholesterol efflux from macrophage cells. Detected in HDL, LDL and VLDL. Secreted by a microsomal triglyceride transfer protein (MTTP)-dependent mechanism, probably as a VLDL-associated protein that is subsequently transferred to HDL (PubMed:16956892). {ECO:0000269|PubMed:16956892, ECO:0000269|PubMed:24743151, ECO:0000269|PubMed:25764979}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.365
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.371
• hipred: N
• hipred_score: 0.401
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.378

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apoo
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: lipid transport;cristae formation
• Cellular component: Golgi membrane;extracellular region;extracellular space;mitochondrion;endoplasmic reticulum membrane;cytosol;integral component of mitochondrial inner membrane;very-low-density lipoprotein particle;low-density lipoprotein particle;high-density lipoprotein particle;MICOS complex
• Molecular function: protein binding