AKAP8L

A-kinase anchoring protein 8 like

Basic information

Region (hg38): 19:15380050-15419141

Links

ENSG00000011243 ∙ NCBI:26993 ∙ OMIM:609475 ∙ HGNC:29857 ∙ Uniprot:Q9ULX6 ∙ 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 AKAP8L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AKAP8L 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	2
missense			39		1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	39	1	2

Variants in AKAP8L

This is a list of pathogenic ClinVar variants found in the AKAP8L region.

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

Position	Type	Phenotype	Significance	ClinVar
19-15380133-C-T		not specified	Uncertain significance (Mar 28, 2024)
19-15380164-G-C			Likely benign (May 25, 2018)
19-15380181-G-A		not specified	Uncertain significance (Apr 08, 2022)
19-15380249-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-15380271-C-G		not specified	Uncertain significance (Jul 14, 2021)
19-15380373-C-T		not specified	Uncertain significance (Jun 06, 2023)
19-15380387-T-G		not specified	Uncertain significance (Aug 08, 2022)
19-15380539-T-C		not specified	Uncertain significance (Feb 16, 2023)
19-15380549-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-15380593-T-C		not specified	Uncertain significance (Dec 22, 2023)
19-15397215-T-C		not specified	Uncertain significance (Aug 16, 2022)
19-15397242-C-T		not specified	Uncertain significance (Jan 22, 2024)
19-15397270-C-T		not specified	Uncertain significance (Apr 19, 2024)
19-15397577-C-T		not specified	Uncertain significance (Sep 15, 2021)
19-15397619-C-T		not specified	Uncertain significance (Oct 25, 2022)
19-15397755-C-T		not specified	Uncertain significance (Aug 26, 2022)
19-15399408-C-G			Benign (Dec 31, 2019)
19-15400808-T-C		not specified	Uncertain significance (Feb 14, 2023)
19-15400811-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-15400817-C-A		not specified	Uncertain significance (Mar 22, 2023)
19-15400820-C-G		not specified	Uncertain significance (Oct 14, 2023)
19-15400822-G-A		not specified	Uncertain significance (Aug 02, 2022)
19-15400850-C-A		not specified	Uncertain significance (Oct 25, 2023)
19-15400979-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-15401047-G-A			Likely benign (Apr 18, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AKAP8L	protein_coding	protein_coding	ENST00000397410	14	39094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0288	0.971	124626	0	19	124645	0.0000762

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	335	393	0.853	0.0000243	4247
Missense in Polyphen		74	118.37	0.62518		1354
Synonymous	0.278	146	150	0.971	0.00000998	1191
Loss of Function	4.04	10	36.2	0.276	0.00000190	405

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000252	0.000252
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000529	0.0000464
European (Non-Finnish)	0.0000731	0.0000708
Middle Eastern	0.000111	0.000111
South Asian	0.0000655	0.0000654
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could play a role in constitutive transport element (CTE)-mediated gene expression by association with DHX9. Increases CTE-dependent nuclear unspliced mRNA export (PubMed:10748171, PubMed:11402034). Proposed to target PRKACA to the nucleus but does not seem to be implicated in the binding of regulatory subunit II of PKA (PubMed:10761695, PubMed:11884601). May be involved in nuclear envelope breakdown and chromatin condensation. May be involved in anchoring nuclear membranes to chromatin in interphase and in releasing membranes from chromating at mitosis (PubMed:11034899). May regulate the initiation phase of DNA replication when associated with TMPO isoform Beta (PubMed:12538639). Required for cell cycle G2/M transition and histone deacetylation during mitosis. In mitotic cells recruits HDAC3 to the vicinity of chromatin leading to deacetylation and subsequent phosphorylation at 'Ser-10' of histone H3; in this function seems to act redundantly with AKAP8 (PubMed:16980585). May be involved in regulation of pre-mRNA splicing (PubMed:17594903). {ECO:0000269|PubMed:10748171, ECO:0000269|PubMed:11034899, ECO:0000269|PubMed:11402034, ECO:0000269|PubMed:11884601, ECO:0000269|PubMed:12538639, ECO:0000269|PubMed:16980585, ECO:0000305|PubMed:10761695}.; FUNCTION: (Microbial infection) Can synergize with DHX9 to activate the CTE-mediated gene expression of type D retroviruses. {ECO:0000269|PubMed:11402034}.
• Pathway: Epstein-Barr virus infection - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.227
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.0948
• hipred: Y
• hipred_score: 0.731
• ghis: 0.649

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.979

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Akap8l

Gene ontology

• Biological process: mRNA processing;mitotic chromosome condensation;RNA splicing;regulation of mRNA export from nucleus;positive regulation of histone deacetylation;regulation of histone phosphorylation;cell cycle G2/M phase transition;positive regulation of transcription by RNA polymerase II;nuclear envelope disassembly
• Cellular component: chromatin;nucleus;cytoplasm;nuclear matrix;PML body;nuclear speck;ribonucleoprotein complex
• Molecular function: DNA binding;RNA binding;protein binding;lamin binding;DEAD/H-box RNA helicase binding;protein kinase A regulatory subunit binding;histone deacetylase binding;metal ion binding