APOM

apolipoprotein M, the group of Lipocalins|Apolipoproteins

Basic information

Region (hg38): 6:31652416-31658210

Links

ENSG00000204444 ∙ NCBI:55937 ∙ OMIM:606907 ∙ HGNC:13916 ∙ Uniprot:O95445 ∙ 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 APOM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOM 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						0
missense			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					1	1
Total	0	0	7	1	1

Variants in APOM

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

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

Position	Type	Phenotype	Significance	ClinVar
6-31655039-T-C			Benign (Nov 02, 2023)
6-31656036-C-A		not specified	Uncertain significance (Aug 13, 2021)
6-31656593-C-T		not specified	Uncertain significance (Nov 30, 2021)
6-31656597-G-A		not specified	Uncertain significance (Dec 15, 2023)
6-31656615-TACCATCCGCATGTGAGTGGTAAGGAGGCAGAAGCATC-T			Uncertain significance (Jul 02, 2020)
6-31656623-G-C		not specified	Uncertain significance (Sep 17, 2021)
6-31657440-A-T		not specified	Uncertain significance (Aug 02, 2023)
6-31657457-T-A		not specified	Uncertain significance (May 18, 2023)
6-31657645-G-A		not specified	Likely benign (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOM	protein_coding	protein_coding	ENST00000375916	6	5795

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000956	0.823	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.935	80	107	0.746	0.00000590	1228
Missense in Polyphen		36	42.009	0.85697		436
Synonymous	0.955	31	38.5	0.804	0.00000197	356
Loss of Function	1.16	6	9.94	0.604	4.21e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000449	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in lipid transport. Can bind sphingosine-1-phosphate, myristic acid, palmitic acid and stearic acid, retinol, all-trans-retinoic acid and 9-cis-retinoic acid. {ECO:0000269|PubMed:17525477, ECO:0000269|PubMed:19733574}.
• Pathway: Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism;Metabolism of vitamins and cofactors;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.473
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.688
• hipred: N
• hipred_score: 0.170
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apom
• Phenotype: homeostasis/metabolism phenotype; reproductive system phenotype

Gene ontology

• Biological process: retinoid metabolic process;response to glucose;cholesterol efflux;high-density lipoprotein particle remodeling;high-density lipoprotein particle assembly;high-density lipoprotein particle clearance;negative regulation of plasma lipoprotein oxidation;lipoprotein metabolic process;cholesterol homeostasis;reverse cholesterol transport;cellular oxidant detoxification
• Cellular component: extracellular region;very-low-density lipoprotein particle;low-density lipoprotein particle;high-density lipoprotein particle;discoidal high-density lipoprotein particle;spherical high-density lipoprotein particle
• Molecular function: lipid transporter activity;phospholipid binding;antioxidant activity