AKAP3

A-kinase anchoring protein 3, the group of A-kinase anchoring proteins

Basic information

Region (hg38): 12:4615508-4649051

Links

ENSG00000111254 ∙ NCBI:10566 ∙ OMIM:604689 ∙ HGNC:373 ∙ Uniprot:O75969 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 82 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 82	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	35228300

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AKAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AKAP3 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			51	5		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	51	5	3

Variants in AKAP3

This is a list of pathogenic ClinVar variants found in the AKAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-4615800-T-C		not specified	Uncertain significance (Jan 10, 2023)
12-4615829-C-T			Benign (Nov 01, 2022)
12-4615831-C-A		not specified	Uncertain significance (Apr 17, 2024)
12-4615846-C-T		not specified	Uncertain significance (Jan 17, 2023)
12-4615873-C-T		not specified	Uncertain significance (Jan 23, 2024)
12-4626614-TTG-T		Spermatogenic failure 82	Pathogenic (Dec 14, 2023)
12-4626621-T-C		not specified	Uncertain significance (Jan 03, 2022)
12-4626723-C-T		not specified	Uncertain significance (Jan 16, 2024)
12-4626765-T-C		not specified	Uncertain significance (Feb 28, 2023)
12-4626779-G-A		not specified	Uncertain significance (Mar 18, 2024)
12-4626947-C-G		not specified	Uncertain significance (Apr 06, 2022)
12-4626962-G-A		not specified	Uncertain significance (Oct 26, 2021)
12-4626980-T-A		not specified	Uncertain significance (May 05, 2023)
12-4627034-T-A		not specified	Uncertain significance (Jun 09, 2022)
12-4627038-C-T		not specified	Uncertain significance (Mar 14, 2023)
12-4627044-G-C		not specified	Uncertain significance (Nov 13, 2023)
12-4627049-G-A		not specified	Uncertain significance (Dec 05, 2022)
12-4627107-G-A		not specified	Uncertain significance (Oct 26, 2022)
12-4627140-T-C		not specified	Uncertain significance (Mar 15, 2024)
12-4627173-G-C		not specified	Uncertain significance (Nov 18, 2022)
12-4627277-C-T		not specified	Uncertain significance (Aug 28, 2023)
12-4627349-T-C		not specified	Likely benign (Aug 13, 2021)
12-4627365-G-A		not specified	Uncertain significance (Jan 23, 2023)
12-4627487-A-G		not specified	Likely benign (Jun 21, 2022)
12-4627541-A-T		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AKAP3	protein_coding	protein_coding	ENST00000545990	3	33540

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0564	0.943	94395	2566	28787	125748	0.134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.468	441	470	0.939	0.0000248	5618
Missense in Polyphen		167	184.05	0.90734		2389
Synonymous	1.42	160	184	0.867	0.0000104	1678
Loss of Function	3.32	7	24.9	0.281	0.00000121	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.482	0.360
Ashkenazi Jewish	0.256	0.127
East Asian	0.267	0.133
Finnish	0.165	0.0829
European (Non-Finnish)	0.244	0.120
Middle Eastern	0.267	0.133
South Asian	0.515	0.255
Other	0.269	0.133

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a regulator of both motility- and head- associated functions such as capacitation and the acrosome reaction.
• Pathway: G Protein Signaling Pathways (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.775
• rvis_EVS: 1.21
• rvis_percentile_EVS: 93.03

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.300
• ghis: 0.381

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.420

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Akap3

Gene ontology

• Biological process: blastocyst hatching;transmembrane receptor protein serine/threonine kinase signaling pathway;single fertilization;acrosome reaction;protein localization
• Cellular component: acrosomal vesicle;nucleus;cytoplasm;sperm fibrous sheath;sperm principal piece
• Molecular function: protein binding;protein kinase A binding