AKAP17A

protein-coding

A-kinase anchoring protein 17A, the group of Pseudoautosomal region 1|A-kinase anchoring proteins

Gene summary

This locus encodes a protein kinase A anchoring protein. The encoded protein is part of the spliceosome complex and is involved in the regulation of alternate splicing in some mRNA precursors. Alternatively spliced transcript variants have been identified for this gene.[provided by RefSeq, Sep 2010]

Previous symbols:

CXYorf3
SFRS17A

MANE transcript

N/A

Inheritance

—

ClinVar variants

—

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chrY:1,591,604-1,602,520

External References & Databases

Ensembl (ENSG00000292343)

NCBI Gene (8227)

OMIM (312095, 465000)

Transcript & Mutation Effects

hg38 • Region Span ~10.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AKAP17A variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB
synonymous
missense
nonsense
start loss
frameshift
splice donor/acceptor (+/-2bp)
Total	0	0	0	0	0

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
ENST00000313871.9	Ensembl	ENSP00000324827.3	4	MANE Select
NM_005088.3	RefSeq	NP_005079.2	8	Standard
ENST00000381261.8	Ensembl	ENSP00000370660.3	3	Standard
ENST00000381261.9	Ensembl	ENSP00000370660.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
mRNA processing
signal transduction
RNA splicing
B cell activation

Molecular Function

RNA binding
protein binding
protein kinase A binding

Cellular Component

nucleus
spliceosomal complex
cytosol
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000313871
Coding exons: 4
Length: 10922
Individuals with no LoFs: 125582
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125589
p: 0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.279	446	463	0.963	0.0000356	4496
Missense (PolyPhen)		47	104.66	0.44908		1061
Synonymous	-2.82	259	207	1.25	0.0000164	1370
Loss of Function	2.84	3	14.8	0.203	8.10e-7	173

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000032	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Splice factor regulating alternative splice site selection for certain mRNA precursors. Mediates regulation of pre- mRNA splicing in a PKA-dependent manner. {ECO:0000269|PubMed:16982639, ECO:0000269|PubMed:19840947}.;

Recessive Scores

pRec: 0.128

Intolerance Scores

RVIS EVS: -0.63
RVIS percentile EVS: 16.78

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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