REG3A

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

Basic information

Region (hg38): 2:79157003-79159753

Previous symbols: [ "PAP" ]

Links

ENSG00000172016 ∙ NCBI:5068 ∙ OMIM:167805 ∙ HGNC:8601 ∙ Uniprot:Q06141 ∙ 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 REG3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REG3A 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				3	2	5
missense			9	4		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	9	7	2

Variants in REG3A

This is a list of pathogenic ClinVar variants found in the REG3A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-79157247-A-G			Likely benign (Jan 30, 2018)
2-79157287-A-C		not specified	Uncertain significance (Nov 07, 2024)
2-79157290-A-G		not specified	Uncertain significance (Mar 08, 2025)
2-79157582-C-T			Benign (Dec 19, 2017)
2-79157589-C-T		not specified	Uncertain significance (Feb 28, 2024)
2-79157592-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-79157623-G-C		not specified	Uncertain significance (Aug 19, 2024)
2-79157653-C-T		not specified	Uncertain significance (Nov 25, 2024)
2-79157658-C-G		not specified	Likely benign (Aug 10, 2023)
2-79157678-T-A		not specified	Likely benign (Aug 04, 2023)
2-79157685-T-C		not specified	Uncertain significance (May 09, 2024)
2-79158334-G-A		not specified	Uncertain significance (Jan 08, 2024)
2-79158337-C-G		not specified	Uncertain significance (Feb 28, 2025)
2-79158355-C-T		not specified	Likely benign (Jun 11, 2021)
2-79158414-C-T		not specified	Uncertain significance (Aug 19, 2024)
2-79158660-T-C			Likely benign (Jan 02, 2018)
2-79158703-C-A		not specified	Uncertain significance (Feb 23, 2023)
2-79159337-C-T			Benign (Dec 31, 2019)
2-79159375-A-T			Likely benign (Jun 05, 2018)
2-79159400-C-A			Likely benign (Aug 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REG3A	protein_coding	protein_coding	ENST00000393878	5	2748

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000629	0.746	125724	0	12	125736	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.203	103	97.4	1.06	0.00000517	1122
Missense in Polyphen		18	28.863	0.62363		375
Synonymous	-0.601	44	39.2	1.12	0.00000210	337
Loss of Function	0.947	6	9.08	0.661	3.86e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000521	0.000521
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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. Regulates keratinocyte proliferation and differentiation after skin injury via activation of EXTL3-PI3K-AKT signaling pathway. {ECO:0000269|PubMed:16931762}.
• Pathway: Purine metabolism;Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.910
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.195
• hipred: N
• hipred_score: 0.112
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.643

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Reg3b
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: acute-phase response;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;multicellular organism development;cell population proliferation;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;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;protein binding;carbohydrate binding;identical protein binding;peptidoglycan binding;oligosaccharide binding