APOL4

apolipoprotein L4, the group of Apolipoproteins

Basic information

Region (hg38): 22:36189123-36204840

Links

ENSG00000100336 ∙ NCBI:80832 ∙ OMIM:607254 ∙ HGNC:14867 ∙ Uniprot:Q9BPW4 ∙ 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 APOL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOL4 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			5	2		7
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	3	0

Variants in APOL4

This is a list of pathogenic ClinVar variants found in the APOL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-36191219-A-T		not specified	Uncertain significance (May 03, 2024)
22-36191797-A-ACT			Likely benign (Jun 26, 2017)
22-36191892-T-C		not specified	Uncertain significance (Aug 02, 2021)
22-36195395-T-A		not specified	Uncertain significance (Dec 13, 2022)
22-36195428-C-T		not specified	Uncertain significance (Jul 20, 2021)
22-36199331-T-G		not specified	Likely benign (Dec 18, 2023)
22-36199341-C-T		not specified	Uncertain significance (Sep 16, 2021)
22-36199375-C-T		not specified	Likely benign (Jul 14, 2023)
22-36201996-A-T		not specified	Uncertain significance (Jun 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOL4	protein_coding	protein_coding	ENST00000352371	5	15715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00107	0.622	125433	0	24	125457	0.0000957

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0220	189	188	1.00	0.0000100	2243
Missense in Polyphen		35	49.72	0.70394		629
Synonymous	-1.35	87	72.4	1.20	0.00000389	717
Loss of Function	0.567	5	6.57	0.761	2.78e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000233	0.000233
Ashkenazi Jewish	0.00	0.00
East Asian	0.000438	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000528
Middle Eastern	0.000438	0.000435
South Asian	0.0000327	0.0000327
Other	0.000168	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in lipid exchange and transport throughout the body. May participate in reverse cholesterol transport from peripheral cells to the liver (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0795

Haploinsufficiency Scores

• pHI: 0.0718
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Gene ontology

• Biological process: lipid metabolic process;lipid transport;lipoprotein metabolic process
• Cellular component: cellular_component;extracellular space;intracellular membrane-bounded organelle
• Molecular function: molecular_function;lipid binding