PREX1

phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1, the group of Dbl family Rho GEFs|PDZ domain containing|Pleckstrin homology domain containing

Basic information

Region (hg38): 20:48624252-48827999

Links

ENSG00000124126 ∙ NCBI:57580 ∙ OMIM:606905 ∙ HGNC:32594 ∙ Uniprot:Q8TCU6 ∙ 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 PREX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PREX1 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				5	6	11
missense			70	7	2	79
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	70	12	8

Variants in PREX1

This is a list of pathogenic ClinVar variants found in the PREX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-48625893-C-T		not specified	Uncertain significance (Aug 02, 2022)
20-48625904-G-A		not specified	Uncertain significance (Jun 26, 2024)
20-48627563-G-A		not specified	Uncertain significance (Jun 11, 2024)
20-48627879-C-T			Benign (Oct 27, 2017)
20-48627880-G-A		not specified	Uncertain significance (May 17, 2023)
20-48627888-C-A		not specified	Uncertain significance (Sep 01, 2021)
20-48627913-T-C		not specified	Uncertain significance (Mar 18, 2024)
20-48627919-C-T		not specified	Uncertain significance (Nov 12, 2024)
20-48627929-T-C		not specified	Uncertain significance (Aug 11, 2024)
20-48629509-G-A		not specified	Uncertain significance (Dec 19, 2022)
20-48629536-A-C		not specified	Uncertain significance (Dec 28, 2023)
20-48629539-C-G			Benign (Dec 14, 2018)
20-48629549-C-T		not specified	Uncertain significance (Feb 01, 2023)
20-48629589-G-A			Benign (Dec 14, 2018)
20-48629611-G-C		not specified	Uncertain significance (Aug 26, 2024)
20-48630735-A-C		not specified	Uncertain significance (Sep 04, 2024)
20-48630741-A-C		not specified	Uncertain significance (Sep 04, 2024)
20-48630753-C-A		not specified	Uncertain significance (Jun 21, 2023)
20-48630762-G-A		not specified	Uncertain significance (Feb 08, 2023)
20-48630769-G-C		not specified	Uncertain significance (Nov 18, 2022)
20-48630778-G-A		not specified	Uncertain significance (Jul 25, 2023)
20-48632347-C-A			Benign/Likely benign (Nov 01, 2022)
20-48632362-G-C		not specified	Uncertain significance (Sep 25, 2024)
20-48632516-T-C		not specified	Uncertain significance (Apr 19, 2024)
20-48632539-C-T			Benign (Aug 20, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PREX1	protein_coding	protein_coding	ENST00000371941	40	203631

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.56e-12	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.69	669	997	0.671	0.0000632	10897
Missense in Polyphen		162	342.73	0.47268		3652
Synonymous	1.19	390	421	0.926	0.0000285	3184
Loss of Function	8.26	3	85.3	0.0352	0.00000407	1006

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000968	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol 3,4,5-trisphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.
• Pathway: Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Chemokine signaling pathway;Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Regulation of RAC1 activity;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;Cell death signalling via NRAGE, NRIF and NADE (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.0897
• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.749
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prex1
• Phenotype: growth/size/body region phenotype; cellular phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; hematopoietic system 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)

Zebrafish Information Network

• Gene name: prex1
• Affected structure: GTPase activity
• Phenotype tag: abnormal
• Phenotype quality: decreased process quality

Gene ontology

• Biological process: superoxide metabolic process;G protein-coupled receptor signaling pathway;actin filament polymerization;T cell differentiation;positive regulation of cell migration;neutrophil chemotaxis;regulation of actin filament polymerization;regulation of Rho protein signal transduction;intracellular signal transduction;neutrophil activation;positive regulation of apoptotic process;positive regulation of GTPase activity;regulation of dendrite development;regulation of small GTPase mediated signal transduction;positive regulation of substrate adhesion-dependent cell spreading
• Cellular component: cytosol;plasma membrane;growth cone;dendritic shaft;perinuclear region of cytoplasm
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity;protein binding;phospholipid binding;enzyme binding;Rac guanyl-nucleotide exchange factor activity