LRG1

leucine rich alpha-2-glycoprotein 1

Basic information

Region (hg38): 19:4536402-4540036

Links

ENSG00000171236 ∙ NCBI:116844 ∙ OMIM:611289 ∙ HGNC:29480 ∙ Uniprot:P02750 ∙ 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 LRG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRG1 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						0
missense			36	5		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	5	0

Variants in LRG1

This is a list of pathogenic ClinVar variants found in the LRG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4538001-C-T		not specified	Uncertain significance (Aug 05, 2024)
19-4538013-T-G		not specified	Uncertain significance (Feb 25, 2025)
19-4538035-G-T		not specified	Uncertain significance (Dec 04, 2024)
19-4538044-G-A		not specified	Uncertain significance (Aug 14, 2023)
19-4538124-T-C		not specified	Uncertain significance (May 09, 2023)
19-4538155-C-T		not specified	Likely benign (Dec 27, 2022)
19-4538166-G-T		not specified	Uncertain significance (Jul 16, 2024)
19-4538188-C-A		not specified	Uncertain significance (Nov 08, 2022)
19-4538192-C-A		not specified	Uncertain significance (May 09, 2022)
19-4538199-A-G		not specified	Uncertain significance (Mar 06, 2023)
19-4538224-C-T		not specified	Uncertain significance (Oct 20, 2024)
19-4538230-C-T		not specified	Uncertain significance (Jan 18, 2025)
19-4538247-T-C		not specified	Uncertain significance (Dec 10, 2024)
19-4538251-C-G		not specified	Uncertain significance (Sep 27, 2021)
19-4538265-T-A		not specified	Uncertain significance (Mar 08, 2024)
19-4538296-C-G		not specified	Uncertain significance (Sep 20, 2023)
19-4538305-G-C		not specified	Uncertain significance (Jul 14, 2023)
19-4538355-C-A		not specified	Uncertain significance (Jan 26, 2022)
19-4538364-A-G		not specified	Uncertain significance (Mar 07, 2024)
19-4538371-G-C		not specified	Uncertain significance (Sep 05, 2024)
19-4538400-A-G		not specified	Uncertain significance (Aug 08, 2023)
19-4538440-C-T		not specified	Uncertain significance (Nov 18, 2022)
19-4538446-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-4538454-C-T		not specified	Likely benign (Apr 08, 2024)
19-4538460-C-T		not specified	Uncertain significance (Feb 26, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRG1	protein_coding	protein_coding	ENST00000306390	2	4066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0951	0.591	125747	0	1	125748	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0461	203	201	1.01	0.0000129	2197
Missense in Polyphen		59	58.046	1.0164		768
Synonymous	-0.648	110	102	1.08	0.00000683	787
Loss of Function	0.0691	1	1.08	0.928	4.58e-8	12

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.583
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.41

Haploinsufficiency Scores

• pHI: 0.0987
• hipred: N
• hipred_score: 0.146
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.285

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrg1
• Phenotype: neoplasm

Gene ontology

• Biological process: positive regulation of endothelial cell proliferation;biological_process;response to bacterium;positive regulation of transforming growth factor beta receptor signaling pathway;neutrophil degranulation;positive regulation of angiogenesis;brown fat cell differentiation
• Cellular component: extracellular region;extracellular space;membrane;specific granule lumen;intracellular membrane-bounded organelle;extracellular exosome;tertiary granule lumen;ficolin-1-rich granule lumen
• Molecular function: molecular_function;transforming growth factor beta receptor binding;protein binding