REG1B

regenerating family member 1 beta, the group of C-type lectin domain containing

Basic information

Region (hg38): 2:79085023-79088019

Links

ENSG00000172023 ∙ NCBI:5968 ∙ OMIM:167771 ∙ HGNC:9952 ∙ Uniprot:P48304 ∙ 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 REG1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REG1B 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			9	1		10
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	1	0

Variants in REG1B

This is a list of pathogenic ClinVar variants found in the REG1B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-79085233-A-C		not specified	Uncertain significance (Apr 04, 2024)
2-79085239-A-G		not specified	Uncertain significance (Apr 22, 2022)
2-79085261-T-A		not specified	Uncertain significance (Apr 18, 2024)
2-79085596-C-A		not specified	Uncertain significance (Jun 16, 2024)
2-79086426-T-C		not specified	Likely benign (Dec 17, 2021)
2-79086452-G-A		not specified	Uncertain significance (Nov 22, 2021)
2-79086471-C-A		not specified	Uncertain significance (Oct 26, 2021)
2-79086482-G-A		not specified	Uncertain significance (Feb 16, 2023)
2-79086485-T-A		not specified	Uncertain significance (Jun 22, 2023)
2-79086832-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-79086850-A-C		not specified	Uncertain significance (Aug 12, 2021)
2-79087596-G-A		not specified	Uncertain significance (Aug 23, 2021)
2-79087596-G-C		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REG1B	protein_coding	protein_coding	ENST00000305089	5	2990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000195	0.273	125594	0	97	125691	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	116	88.5	1.31	0.00000450	1094
Missense in Polyphen		12	15.098	0.7948		166
Synonymous	-0.559	39	34.8	1.12	0.00000183	293
Loss of Function	0.165	9	9.55	0.942	4.95e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00344	0.00344
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.000327	0.000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Might act as an inhibitor of spontaneous calcium carbonate precipitation. May be associated with neuronal sprouting in brain, and with brain and pancreas regeneration.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.802
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.112
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.571

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Reg2
• 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: cell population proliferation;positive regulation of cell population proliferation;response to peptide hormone;cell wall disruption in other organism;antimicrobial humoral immune response mediated by antimicrobial peptide
• Cellular component: extracellular space;extracellular exosome
• Molecular function: transmembrane signaling receptor activity;peptidoglycan binding;oligosaccharide binding