PRKX

protein kinase cAMP-dependent X-linked catalytic subunit, the group of AGC family kinases

Basic information

Region (hg38): X:3604340-3713649

Links

ENSG00000183943 ∙ NCBI:5613 ∙ OMIM:300083 ∙ HGNC:9441 ∙ Uniprot:P51817 ∙ 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 PRKX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRKX 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	1	3
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	17	4	3

Variants in PRKX

This is a list of pathogenic ClinVar variants found in the PRKX 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-3612234-G-A		not specified	Uncertain significance (Aug 15, 2023)
X-3612243-G-A		not specified	Uncertain significance (Apr 26, 2023)
X-3612253-C-T		not specified	Likely benign (Jun 22, 2023)
X-3612296-G-A			Benign (Nov 24, 2017)
X-3612308-C-G		not specified	Uncertain significance (Mar 29, 2022)
X-3612316-C-T		not specified	Uncertain significance (Sep 19, 2022)
X-3612334-C-T			Benign (Oct 06, 2017)
X-3615805-T-A			Benign (Jun 13, 2018)
X-3615831-G-A		not specified	Uncertain significance (Oct 05, 2022)
X-3615850-C-T		not specified	Uncertain significance (Jun 05, 2024)
X-3615853-A-T		not specified	Uncertain significance (Sep 15, 2021)
X-3615856-G-A		not specified	Uncertain significance (Dec 21, 2023)
X-3615864-C-T		not specified	Uncertain significance (Nov 15, 2021)
X-3615865-G-A		not specified	Uncertain significance (Feb 28, 2023)
X-3626461-G-C		not specified	Uncertain significance (Dec 31, 2023)
X-3655314-G-C		not specified	Uncertain significance (May 17, 2023)
X-3655321-G-A		not specified	Uncertain significance (Sep 27, 2021)
X-3655327-G-A		not specified	Uncertain significance (Feb 16, 2023)
X-3655354-C-T		not specified	Uncertain significance (Feb 23, 2023)
X-3655358-C-T			Likely benign (Aug 01, 2022)
X-3655390-G-A		not specified	Uncertain significance (Mar 29, 2022)
X-3655393-C-T		not specified	Uncertain significance (Jul 06, 2021)
X-3655403-C-T			Likely benign (Sep 01, 2022)
X-3713212-G-C			Likely benign (Mar 01, 2023)
X-3713237-A-G		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRKX	protein_coding	protein_coding	ENST00000262848	8	109239

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0326	0.931	125740	1	4	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	93	148	0.630	0.0000132	2362
Missense in Polyphen		26	51.943	0.50055		888
Synonymous	-1.10	78	66.6	1.17	0.00000670	673
Loss of Function	1.80	4	10.2	0.391	7.18e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000135	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000368	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000527	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine protein kinase regulated by and mediating cAMP signaling in cells. Acts through phosphorylation of downstream targets that may include CREB, SMAD6 and PKD1 and has multiple functions in cellular differentiation and epithelial morphogenesis. Regulates myeloid cell differentiation through SMAD6 phosphorylation. Involved in nephrogenesis by stimulating renal epithelial cell migration and tubulogenesis. Also involved in angiogenesis through stimulation of endothelial cell proliferation, migration and vascular-like structure formation. {ECO:0000269|PubMed:12082174, ECO:0000269|PubMed:16236808, ECO:0000269|PubMed:16491121, ECO:0000269|PubMed:17980165, ECO:0000269|PubMed:19367327, ECO:0000269|PubMed:21684272, ECO:0000269|PubMed:9860982}.
• Disease: DISEASE: Note=A chromosomal aberration involving PRKX is a cause of sex reversal disorder. Translocation t(X;Y)(p22;p11) with PRKY. Chromosomal translocations proximal to PRKY account for about 30% of the cases of sex reversal disorder in XX males and XY females.
• Pathway: Chemokine signaling pathway;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.388
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.713
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prkx

Gene ontology

• Biological process: angiogenesis;endothelial cell proliferation;cell adhesion;peptidyl-serine phosphorylation;myeloid cell differentiation;regulation of cell adhesion;regulation of cell migration;cell-substrate adhesion;endothelial cell migration;protein autophosphorylation;epithelial tube morphogenesis;kidney morphogenesis;regulation of epithelial cell differentiation involved in kidney development
• Cellular component: nucleus;cytoplasm
• Molecular function: cAMP-dependent protein kinase activity;protein binding;ATP binding