PXK

PX domain containing serine/threonine kinase like

Basic information

Region (hg38): 3:58332879-58426127

Links

ENSG00000168297 ∙ NCBI:54899 ∙ OMIM:611450 ∙ HGNC:23326 ∙ Uniprot:Q7Z7A4 ∙ 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 PXK gene.

• Inborn genetic diseases (12 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PXK 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
missense			11	1	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	1

Variants in PXK

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

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

Position	Type	Phenotype	Significance	ClinVar
3-58382520-G-A		not specified	Uncertain significance (Mar 22, 2022)
3-58382619-A-T		not specified	Uncertain significance (Dec 01, 2022)
3-58390582-A-G		not specified	Uncertain significance (Feb 28, 2023)
3-58390585-T-A		not specified	Uncertain significance (Feb 03, 2022)
3-58390623-C-T		not specified	Uncertain significance (Aug 12, 2021)
3-58391211-G-A			Benign (Feb 01, 2024)
3-58391800-T-A		not specified	Uncertain significance (Mar 12, 2024)
3-58391835-G-A			Benign/Likely benign (Mar 01, 2023)
3-58395667-A-C		not specified	Uncertain significance (Jun 13, 2023)
3-58397638-C-T		not specified	Uncertain significance (Aug 02, 2022)
3-58397708-C-T		not specified	Uncertain significance (Jan 16, 2024)
3-58397720-T-C		not specified	Uncertain significance (Oct 22, 2021)
3-58399371-A-G		not specified	Uncertain significance (Dec 20, 2023)
3-58403872-G-A		not specified	Uncertain significance (Mar 06, 2023)
3-58403905-T-G		not specified	Uncertain significance (Apr 25, 2023)
3-58409545-G-A		not specified	Uncertain significance (Oct 17, 2023)
3-58410115-A-T			Benign (Feb 20, 2018)
3-58412901-C-G		not specified	Uncertain significance (Jan 30, 2024)
3-58424782-C-G		not specified	Uncertain significance (Sep 20, 2023)
3-58424821-C-A		not specified	Uncertain significance (Jan 08, 2024)
3-58424842-C-T		not specified	Likely benign (Dec 13, 2022)
3-58424866-G-A		not specified	Uncertain significance (Oct 26, 2021)
3-58424908-G-C		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PXK	protein_coding	protein_coding	ENST00000356151	18	93142

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0108	0.989	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	246	299	0.822	0.0000160	3740
Missense in Polyphen		51	76.478	0.66685		960
Synonymous	0.569	108	116	0.933	0.00000675	1093
Loss of Function	4.06	11	38.0	0.290	0.00000229	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.000165	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to and modulates brain Na,K-ATPase subunits ATP1B1 and ATP1B3 and may thereby participate in the regulation of electrical excitability and synaptic transmission. May not display kinase activity. {ECO:0000250|UniProtKB:Q8BX57, ECO:0000303|PubMed:16142408}.

Recessive Scores

• pRec: 0.0984

Intolerance Scores

• loftool: 0.559
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.58

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.426
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pxk

Gene ontology

• Biological process: protein phosphorylation;inflammatory response;negative regulation of ATPase activity;regulation of membrane potential;negative regulation of ion transport;modulation of chemical synaptic transmission
• Cellular component: cytoplasm;microtubule organizing center;cytosol;plasma membrane;protein-containing complex
• Molecular function: nucleotide binding;actin binding;protein kinase activity;ATP binding;phosphatidylinositol binding