PXN

paxillin, the group of LIM domain containing

Basic information

Region (hg38): 12:120210438-120265771

Links

ENSG00000089159 ∙ NCBI:5829 ∙ OMIM:602505 ∙ HGNC:9718 ∙ Uniprot:P49023 ∙ 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 PXN gene.

• Inborn genetic diseases (28 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PXN 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	3	4
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			1		1	2
Total	0	0	27	2	4

Variants in PXN

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

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

Position	Type	Phenotype	Significance	ClinVar
12-120212466-T-C		not specified	Uncertain significance (Mar 01, 2024)
12-120212468-G-A		not specified	Uncertain significance (Aug 02, 2021)
12-120212483-G-A		not specified	Uncertain significance (Mar 02, 2023)
12-120212569-C-T			Benign (Jun 28, 2018)
12-120213873-G-A		not specified	Uncertain significance (Jul 21, 2022)
12-120213880-G-A		not specified	Uncertain significance (Dec 27, 2022)
12-120213957-C-G		not specified	Uncertain significance (Jan 26, 2022)
12-120213982-C-T		not specified	Uncertain significance (Nov 09, 2023)
12-120214210-A-G		not specified	Uncertain significance (Oct 13, 2023)
12-120214839-C-T		not specified	Uncertain significance (Aug 17, 2021)
12-120214855-G-A			Benign (Aug 14, 2018)
12-120214895-G-A		not specified	Uncertain significance (Mar 29, 2022)
12-120214923-G-A		not specified	Uncertain significance (Mar 01, 2023)
12-120215008-A-C			Benign (Apr 24, 2018)
12-120215095-C-T			Benign (Jun 28, 2018)
12-120215132-C-T		not specified	Uncertain significance (May 22, 2023)
12-120215197-A-G		not specified	Uncertain significance (Apr 20, 2023)
12-120215568-C-T		not specified	Uncertain significance (Jul 26, 2022)
12-120215637-C-T		not specified	Uncertain significance (Feb 15, 2023)
12-120215639-G-A		not specified	Uncertain significance (Dec 07, 2023)
12-120215655-C-G		not specified	Uncertain significance (Dec 27, 2022)
12-120221639-G-A		not specified	Uncertain significance (Dec 06, 2022)
12-120221652-C-T		not specified	Uncertain significance (Nov 14, 2023)
12-120221685-T-C		not specified	Uncertain significance (Dec 20, 2021)
12-120221754-C-T		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PXN	protein_coding	protein_coding	ENST00000267257	11	55325

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0823	0.918	124661	0	12	124673	0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	284	369	0.770	0.0000237	3893
Missense in Polyphen		78	120.86	0.64535		1248
Synonymous	0.168	162	165	0.983	0.0000121	1184
Loss of Function	3.45	7	26.0	0.270	0.00000126	315

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000104	0.0000935
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000167
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000568	0.0000531
Middle Eastern	0.000168	0.000167
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion).
• Pathway: Focal adhesion - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Angiogenesis overview;Integrin-mediated Cell Adhesion;Prolactin Signaling Pathway;Androgen Receptor Network in Prostate Cancer;Oncostatin M Signaling Pathway;JAK-STAT;Focal Adhesion;Signaling of Hepatocyte Growth Factor Receptor;Rac1-Pak1-p38-MMP-2 pathway;VEGFA-VEGFR2 Signaling Pathway;Chemokine signaling pathway;Regulation of Actin Cytoskeleton;Smooth Muscle Contraction;Signaling by PTK6;Signal Transduction;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;ucalpain and friends in cell spread;integrin signaling pathway;vegf hypoxia and angiogenesis;mcalpain and friends in cell motility;VEGFA-VEGFR2 Pathway;Prolactin;TCR;Oncostatin_M;AndrogenReceptor;Signaling by EGFR;cell to cell adhesion signaling;Muscle contraction;Integrin;TGF_beta_Receptor;EGFR1;agrin in postsynaptic differentiation;CXCR4-mediated signaling events;GAB1 signalosome;PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases;Signaling by Non-Receptor Tyrosine Kinases;Signaling events regulated by Ret tyrosine kinase;Gastrin;Signaling by VEGF;Angiopoietin receptor Tie2-mediated signaling;Integrin-linked kinase signaling;Localization of the PINCH-ILK-PARVIN complex to focal adhesions;Regulation of cytoskeletal remodeling and cell spreading by IPP complex components;Cell-extracellular matrix interactions;Cell junction organization;Signaling by Receptor Tyrosine Kinases;Cell-Cell communication;a4b7 Integrin signaling;Alpha9 beta1 integrin signaling events;LPA receptor mediated events;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Fc-epsilon receptor I signaling in mast cells;Signaling events mediated by focal adhesion kinase;EPHB forward signaling;IGF1 pathway;Arf6 signaling events;Alpha4 beta1 integrin signaling events;Signaling events mediated by VEGFR1 and VEGFR2;Integrins in angiogenesis (Consensus)

Recessive Scores

• pRec: 0.619

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.93

Haploinsufficiency Scores

• pHI: 0.198
• hipred: Y
• hipred_score: 0.629
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.546

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pxn
• Phenotype: growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: pxnb
• Affected structure: myotome
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: muscle contraction;cell adhesion;cell-matrix adhesion;signal transduction;signal complex assembly;transforming growth factor beta receptor signaling pathway;cellular response to reactive oxygen species;endothelial cell migration;vascular endothelial growth factor receptor signaling pathway;positive regulation of stress fiber assembly;growth hormone receptor signaling pathway
• Cellular component: stress fiber;cytosol;microtubule associated complex;plasma membrane;focal adhesion;cell cortex;lamellipodium
• Molecular function: integrin binding;protein binding;beta-catenin binding;vinculin binding;protein kinase binding;protein phosphatase binding;ubiquitin protein ligase binding;neuropilin binding;metal ion binding