REG3G

regenerating family member 3 gamma, the group of C-type lectin domain containing

Basic information

Region (hg38): 2:79025686-79028505

Links

ENSG00000143954 ∙ NCBI:130120 ∙ OMIM:609933 ∙ HGNC:29595 ∙ Uniprot:Q6UW15 ∙ 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 REG3G gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REG3G 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	2
missense			11	1	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	2

Variants in REG3G

This is a list of pathogenic ClinVar variants found in the REG3G region.

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

Position	Type	Phenotype	Significance	ClinVar
2-79026130-A-T		not specified	Uncertain significance (Feb 17, 2022)
2-79026137-T-C		not specified	Uncertain significance (Oct 10, 2023)
2-79026726-G-A		not specified	Likely benign (Jun 13, 2023)
2-79027048-G-T		not specified	Uncertain significance (Nov 07, 2022)
2-79027049-C-T		not specified	Uncertain significance (Sep 17, 2021)
2-79027055-T-A		not specified	Uncertain significance (Aug 12, 2021)
2-79027063-A-C		not specified	Likely benign (Apr 25, 2022)
2-79027078-C-T			Benign (Jan 19, 2018)
2-79027097-T-C		not specified	Uncertain significance (Sep 14, 2021)
2-79027161-A-T		not specified	Uncertain significance (Sep 06, 2022)
2-79027163-C-T		not specified	Uncertain significance (Sep 27, 2021)
2-79027811-C-T		not specified	Uncertain significance (May 01, 2023)
2-79027823-G-A			Benign (Apr 16, 2018)
2-79027835-A-G		not specified	Uncertain significance (Mar 01, 2023)
2-79027880-A-C		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REG3G	protein_coding	protein_coding	ENST00000272324	5	2820

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-7	0.115	125602	0	101	125703	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.929	117	91.9	1.27	0.00000434	1129
Missense in Polyphen		30	24.217	1.2388		322
Synonymous	-1.08	43	34.9	1.23	0.00000158	327
Loss of Function	-0.308	10	9.00	1.11	3.82e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000727	0.000727
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000476	0.000475
Middle Eastern	0.0000544	0.0000544
South Asian	0.000555	0.000555
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Bactericidal C-type lectin which acts exclusively against Gram-positive bacteria and mediates bacterial killing by binding to surface-exposed carbohydrate moieties of peptidoglycan. Restricts bacterial colonization of the intestinal epithelial surface and consequently limits activation of adaptive immune responses by the microbiota. The uncleaved form has bacteriostatic activity, whereas the cleaved form has bactericidal activity against L.monocytogenes and methicillin-resistant S.aureus. Regulates keratinocyte proliferation and differentiation after skin injury. {ECO:0000269|PubMed:19095652}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0913

Intolerance Scores

• loftool: 0.890
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.0758
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000294

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Reg3g
• Phenotype: digestive/alimentary phenotype; immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: MyD88-dependent toll-like receptor signaling pathway;acute-phase response;positive regulation of cell population proliferation;positive regulation of keratinocyte proliferation;antimicrobial humoral response;response to peptide hormone;cell wall disruption in other organism;negative regulation of keratinocyte differentiation;defense response to Gram-positive bacterium;cytolysis in other organism;antimicrobial humoral immune response mediated by antimicrobial peptide;positive regulation of wound healing
• Cellular component: extracellular region;extracellular space;cytoplasm
• Molecular function: transmembrane signaling receptor activity;peptidoglycan binding;oligosaccharide binding