PAK5

p21 (RAC1) activated kinase 5

Basic information

Region (hg38): 20:9537369-9839076

Previous symbols: [ "PAK7" ]

Links

ENSG00000101349 ∙ NCBI:57144 ∙ OMIM:608038 ∙ HGNC:15916 ∙ Uniprot:Q9P286 ∙ 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 PAK5 gene.

• Inborn genetic diseases (8 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAK5 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	5	6
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	5

Variants in PAK5

This is a list of pathogenic ClinVar variants found in the PAK5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-9539525-G-C		not specified	Uncertain significance (Oct 05, 2023)
20-9539575-T-C		not specified	Uncertain significance (Dec 17, 2023)
20-9542639-C-A		not specified	Uncertain significance (Dec 14, 2023)
20-9542694-C-T		not specified	Uncertain significance (Aug 02, 2022)
20-9542717-C-A		not specified	Uncertain significance (May 04, 2022)
20-9544431-A-G			Benign (Jul 15, 2018)
20-9565907-G-A			Benign (Apr 12, 2022)
20-9566030-A-T		not specified	Uncertain significance (Mar 02, 2023)
20-9566114-C-A		not specified	Uncertain significance (Jul 20, 2021)
20-9566203-C-T		not specified	Uncertain significance (May 16, 2023)
20-9566230-A-G		not specified	Uncertain significance (Aug 30, 2022)
20-9566236-G-C		not specified	Uncertain significance (Sep 26, 2023)
20-9566303-G-A		not specified	Uncertain significance (Jul 20, 2022)
20-9566318-C-G		not specified	Uncertain significance (May 30, 2023)
20-9566318-C-T		not specified	Uncertain significance (Jun 07, 2023)
20-9566375-C-T		not specified	Uncertain significance (Jan 17, 2023)
20-9566376-G-A			Benign (Dec 31, 2019)
20-9580150-G-T		not specified	Uncertain significance (Apr 06, 2022)
20-9580167-T-C		not specified	Uncertain significance (Oct 27, 2022)
20-9580251-G-A		not specified	Uncertain significance (Nov 23, 2022)
20-9580280-C-A		not specified	Uncertain significance (Dec 13, 2023)
20-9580287-C-A		not specified	Uncertain significance (Aug 04, 2023)
20-9580314-T-C		not specified	Uncertain significance (Dec 14, 2023)
20-9580380-T-A		not specified	Uncertain significance (Nov 09, 2022)
20-9580419-G-C		not specified	Uncertain significance (Jan 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAK5	protein_coding	protein_coding	ENST00000378429	8	301654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000228	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	329	413	0.796	0.0000239	4727
Missense in Polyphen		151	230.67	0.65461		2605
Synonymous	0.391	168	175	0.962	0.0000120	1400
Loss of Function	4.76	1	28.4	0.0352	0.00000128	356

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00217	0.000416
European (Non-Finnish)	0.000414	0.000105
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000979	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine protein kinase that plays a role in a variety of different signaling pathways including cytoskeleton regulation, cell migration, proliferation or cell survival. Activation by various effectors including growth factor receptors or active CDC42 and RAC1 results in a conformational change and a subsequent autophosphorylation on several serine and/or threonine residues. Phosphorylates the proto-oncogene RAF1 and stimulates its kinase activity. Promotes cell survival by phosphorylating the BCL2 antagonist of cell death BAD. Phosphorylates CTNND1, probably to regulate cytoskeletal organization and cell morphology. Keeps microtubules stable through MARK2 inhibition and destabilizes the F-actin network leading to the disappearance of stress fibers and focal adhesions. {ECO:0000269|PubMed:12897128, ECO:0000269|PubMed:16014608, ECO:0000269|PubMed:16581795, ECO:0000269|PubMed:18465753, ECO:0000269|PubMed:20564219}.
• Pathway: Focal adhesion - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);Renal cell carcinoma - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Axon guidance - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MET in type 1 papillary renal cell carcinoma;Ras Signaling;Regulation of Actin Cytoskeleton;Developmental Biology;Activation of RAC1;IL-7 signaling;agrin in postsynaptic differentiation;JAK STAT pathway and regulation;EPO signaling;Signaling by ROBO receptors;Axon guidance;VEGF (Consensus)

Recessive Scores

• pRec: 0.233

Intolerance Scores

• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.6

Haploinsufficiency Scores

• pHI: 0.424
• hipred: Y
• hipred_score: 0.819
• ghis: 0.568

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pak7
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of cell growth;apoptotic process;cytoskeleton organization;signal transduction;learning;memory;locomotory behavior;cell population proliferation;cell migration;signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;regulation of MAPK cascade;negative regulation of extrinsic apoptotic signaling pathway
• Cellular component: nucleoplasm;cytoplasm;mitochondrion;synapse
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;Rac GTPase binding