APOL6

apolipoprotein L6, the group of Apolipoproteins

Basic information

Region (hg38): 22:35648446-35668404

Links

ENSG00000221963 ∙ NCBI:80830 ∙ OMIM:607256 ∙ HGNC:14870 ∙ Uniprot:Q9BWW8 ∙ 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 APOL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOL6 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
missense			30	7		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	9	0

Variants in APOL6

This is a list of pathogenic ClinVar variants found in the APOL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-35656439-C-T		not specified	Uncertain significance (Jan 06, 2023)
22-35656459-G-A		not specified	Uncertain significance (Jun 28, 2023)
22-35658646-G-A		not specified	Uncertain significance (Jul 14, 2023)
22-35658661-G-A		not specified	Likely benign (May 24, 2023)
22-35658668-T-C		not specified	Uncertain significance (Dec 18, 2023)
22-35658676-G-A		not specified	Likely benign (Nov 09, 2021)
22-35658741-G-C		not specified	Uncertain significance (Apr 01, 2024)
22-35658780-G-T		not specified	Uncertain significance (Jun 29, 2023)
22-35658798-C-G		not specified	Uncertain significance (May 23, 2023)
22-35658815-C-T		not specified	Likely benign (Sep 17, 2021)
22-35658827-C-G		not specified	Uncertain significance (Jun 03, 2022)
22-35658860-C-T		not specified	Uncertain significance (Nov 15, 2021)
22-35658869-C-A		not specified	Uncertain significance (Dec 01, 2022)
22-35658898-G-A		not specified	Likely benign (Nov 07, 2023)
22-35658939-C-T			Likely benign (Feb 01, 2023)
22-35658959-G-A		not specified	Likely benign (Feb 09, 2023)
22-35658980-A-G		not specified	Uncertain significance (Apr 28, 2022)
22-35658985-C-T		not specified	Uncertain significance (Mar 02, 2023)
22-35658989-C-T		not specified	Likely benign (Jun 02, 2023)
22-35659012-G-A		not specified	Uncertain significance (Apr 26, 2024)
22-35659030-G-A		not specified	Uncertain significance (Jun 02, 2023)
22-35659060-G-C		not specified	Uncertain significance (Dec 27, 2023)
22-35659094-C-A		not specified	Uncertain significance (Jun 02, 2023)
22-35659106-C-A		not specified	Uncertain significance (Jul 06, 2021)
22-35659121-G-A		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOL6	protein_coding	protein_coding	ENST00000409652	2	20015

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0960	0.592	118849	0	1	118850	0.00000421

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00228	197	197	1.00	0.0000120	2218
Missense in Polyphen		50	45.445	1.1002		588
Synonymous	-0.724	91	82.6	1.10	0.00000531	702
Loss of Function	0.0848	1	1.10	0.913	4.66e-8	12

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000921	0.00000921
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May affect the movement of lipids in the cytoplasm or allow the binding of lipids to organelles.

Intolerance Scores

• loftool: 0.579
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.356

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apol6

Gene ontology

• Biological process: lipid transport;lipoprotein metabolic process
• Cellular component: extracellular region;cytoplasm
• Molecular function: lipid binding