AKAP4

A-kinase anchoring protein 4, the group of A-kinase anchoring proteins

Basic information

Region (hg38): X:50190777-50201007

Links

ENSG00000147081 ∙ NCBI:8852 ∙ OMIM:300185 ∙ HGNC:374 ∙ Uniprot:Q5JQC9 ∙ 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 AKAP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AKAP4 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				4		4
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	6	0

Variants in AKAP4

This is a list of pathogenic ClinVar variants found in the AKAP4 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-50190983-C-T		not specified	Uncertain significance (Oct 03, 2022)
X-50192401-T-G		not specified	Uncertain significance (Feb 01, 2023)
X-50192478-A-G			Likely benign (Nov 01, 2023)
X-50192509-T-G		not specified	Uncertain significance (Jan 04, 2024)
X-50192522-C-G		not specified	Uncertain significance (Dec 28, 2023)
X-50192568-G-T		not specified	Uncertain significance (Jan 03, 2024)
X-50192620-T-C		not specified	Uncertain significance (Oct 06, 2022)
X-50192815-A-C		not specified	Uncertain significance (Jun 11, 2021)
X-50192825-C-T			Uncertain significance (-)
X-50192844-T-A		not specified	Uncertain significance (May 13, 2024)
X-50192872-T-C		not specified	Uncertain significance (Jan 17, 2024)
X-50192921-C-T		not specified	Likely benign (Jul 08, 2022)
X-50192935-G-A		not specified	Uncertain significance (Jun 16, 2023)
X-50193372-T-C			Likely benign (Aug 01, 2022)
X-50193427-C-T		not specified	Uncertain significance (Jun 06, 2023)
X-50193445-A-G		not specified	Uncertain significance (Nov 09, 2023)
X-50193504-A-G			Likely benign (May 01, 2022)
X-50193546-G-T		not specified	Uncertain significance (Dec 27, 2023)
X-50193556-C-A		not specified	Uncertain significance (Jan 19, 2024)
X-50193800-C-T		not specified	Uncertain significance (Mar 27, 2023)
X-50193904-A-G		not specified	Uncertain significance (Oct 25, 2022)
X-50193911-T-C		not specified	Uncertain significance (Dec 01, 2022)
X-50193913-G-A		not specified	Likely benign (Jul 06, 2021)
X-50193932-T-G		not specified	Uncertain significance (Dec 07, 2021)
X-50194118-G-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AKAP4	protein_coding	protein_coding	ENST00000358526	6	10259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00677	124167	1	1	124169	0.00000805

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.784	270	309	0.875	0.0000219	5701
Missense in Polyphen		65	104.83	0.62005		2221
Synonymous	-0.204	120	117	1.02	0.00000874	1589
Loss of Function	3.86	1	19.3	0.0518	0.00000129	397

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000382	0.0000382
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000537	0.0000334
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major structural component of sperm fibrous sheath. Plays a role in sperm motility. {ECO:0000269|PubMed:9822690}.
• Pathway: G Protein Signaling Pathways (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.100
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.61

Haploinsufficiency Scores

• pHI: 0.113
• hipred: Y
• hipred_score: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.444

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Akap4
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: signal transduction;transmembrane receptor protein serine/threonine kinase signaling pathway;single fertilization;flagellated sperm motility;motile cilium assembly;establishment of protein localization
• Cellular component: nucleus;cytoplasm;cytoskeleton;cAMP-dependent protein kinase complex;Z disc;motile cilium;sperm fibrous sheath;perinuclear region of cytoplasm;sperm principal piece
• Molecular function: protein binding;protein kinase A binding