LPXN

leupaxin, the group of LIM domain containing

Basic information

Region (hg38): 11:58526871-58578220

Links

ENSG00000110031 ∙ NCBI:9404 ∙ OMIM:605390 ∙ HGNC:14061 ∙ Uniprot:O60711 ∙ 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 LPXN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPXN 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	19	2	0

Variants in LPXN

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

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

Position	Type	Phenotype	Significance	ClinVar
11-58527677-C-T		not specified	Uncertain significance (Jul 09, 2021)
11-58527699-C-T		not specified	Uncertain significance (Apr 11, 2023)
11-58527715-G-A			Likely benign (Feb 01, 2023)
11-58528072-C-G		not specified	Uncertain significance (Oct 12, 2022)
11-58528135-A-G		not specified	Uncertain significance (Apr 05, 2023)
11-58528197-G-A			Likely benign (Mar 01, 2023)
11-58549845-T-C		not specified	Uncertain significance (Oct 10, 2023)
11-58550030-G-C		not specified	Likely benign (Jun 13, 2023)
11-58550049-C-A		not specified	Uncertain significance (Nov 06, 2023)
11-58550055-C-T		not specified	Uncertain significance (Dec 09, 2023)
11-58550076-C-G		not specified	Uncertain significance (Oct 03, 2022)
11-58550089-T-G		not specified	Uncertain significance (Sep 25, 2023)
11-58551069-C-T		not specified	Uncertain significance (Sep 28, 2022)
11-58551070-C-T		not specified	Uncertain significance (May 24, 2023)
11-58551139-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-58551203-C-G		not specified	Uncertain significance (Aug 30, 2021)
11-58551219-G-T		not specified	Uncertain significance (Jul 21, 2021)
11-58564179-T-C		not specified	Uncertain significance (Feb 26, 2024)
11-58570588-G-A		not specified	Uncertain significance (Feb 22, 2023)
11-58570592-C-G		not specified	Uncertain significance (Oct 05, 2023)
11-58570636-C-T		not specified	Uncertain significance (May 03, 2023)
11-58570707-A-G		not specified	Uncertain significance (Nov 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPXN	protein_coding	protein_coding	ENST00000528954	9	51350

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000191	0.890	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.396	198	214	0.924	0.0000114	2580
Missense in Polyphen		63	83.515	0.75436		1042
Synonymous	0.124	79	80.4	0.982	0.00000423	722
Loss of Function	1.58	12	19.6	0.613	9.14e-7	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000401	0.000398
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000889	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000659	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional coactivator for androgen receptor (AR) and serum response factor (SRF). Contributes to the regulation of cell adhesion, spreading and cell migration and acts as a negative regulator in integrin-mediated cell adhesion events. Suppresses the integrin-induced tyrosine phosphorylation of paxillin (PXN). May play a critical role as an adapter protein in the formation of the adhesion zone in osteoclasts. Negatively regulates B-cell antigen receptor (BCR) signaling. {ECO:0000269|PubMed:17640867, ECO:0000269|PubMed:18451096, ECO:0000269|PubMed:18497331, ECO:0000269|PubMed:20543562}.
• Pathway: TCR;AndrogenReceptor (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.225
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.397
• hipred: N
• hipred_score: 0.229
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0895

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lpxn

Gene ontology

• Biological process: cell adhesion;negative regulation of cell adhesion;signal transduction;regulation of cell adhesion mediated by integrin;negative regulation of B cell receptor signaling pathway;protein-containing complex assembly;regulation of nucleic acid-templated transcription
• Cellular component: podosome;nucleus;cytoplasm;cytosol;plasma membrane;focal adhesion;membrane;nuclear speck;cell projection;perinuclear region of cytoplasm
• Molecular function: transcription coregulator activity;protein binding;metal ion binding