REG1A

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

Basic information

Region (hg38): 2:79120362-79123409

Previous symbols: [ "REG" ]

Links

ENSG00000115386 ∙ NCBI:5967 ∙ OMIM:167770 ∙ HGNC:9951 ∙ Uniprot:P05451 ∙ 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 REG1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REG1A 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	2	3
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	2

Variants in REG1A

This is a list of pathogenic ClinVar variants found in the REG1A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-79120891-G-C			Benign (Dec 13, 2017)
2-79120918-G-C		not specified	Uncertain significance (Dec 21, 2023)
2-79121577-C-G		Focal segmental glomerulosclerosis	Uncertain significance (Nov 01, 2017)
2-79121634-A-G		not specified	Uncertain significance (Apr 01, 2024)
2-79121665-C-T		Kidney disorder	Likely benign (Mar 01, 2018)
2-79121669-G-A		not specified	Uncertain significance (Aug 08, 2023)
2-79122104-T-G		not specified	Uncertain significance (Dec 16, 2023)
2-79122844-C-T		not specified	Uncertain significance (Sep 15, 2021)
2-79122907-A-G		not specified	Uncertain significance (Jan 17, 2024)
2-79122908-G-A		not specified	Likely benign (Dec 02, 2022)
2-79123163-A-G		not specified	Uncertain significance (Mar 22, 2023)
2-79123164-G-A			Benign (Oct 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REG1A	protein_coding	protein_coding	ENST00000233735	5	3058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000135	0.408	125725	0	9	125734	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.309	84	92.3	0.910	0.00000493	1099
Missense in Polyphen		19	28.187	0.67408		344
Synonymous	-1.11	41	32.9	1.25	0.00000160	291
Loss of Function	0.379	8	9.24	0.866	3.96e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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.
• Pathway: Insulin Signaling;Type II interferon signaling (IFNG) (Consensus)

Recessive Scores

• pRec: 0.212

Intolerance Scores

• loftool: 0.700
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

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: response to hypoxia;midgut development;positive regulation of cell population proliferation;negative regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of gene expression;response to nutrient levels;wound healing;response to peptide hormone;cell wall disruption in other organism;protein homotetramerization;calcium ion homeostasis;antimicrobial humoral immune response mediated by antimicrobial peptide;liver regeneration;response to acetylsalicylate;positive regulation of dendrite extension;positive regulation of type B pancreatic cell proliferation;positive regulation of acinar cell proliferation;response to water-immersion restraint stress;pancreas regeneration;response to growth hormone-releasing hormone;cellular response to chemokine;cellular response to gastrin
• Cellular component: extracellular space;cytosol;growth cone;dendrite membrane;neuronal cell body membrane;protein-containing complex;zymogen granule;basal part of cell;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: transmembrane signaling receptor activity;growth factor activity;protein phosphatase binding;protein homodimerization activity;peptidoglycan binding;oligosaccharide binding