REG4

regenerating family member 4, the group of C-type lectin domain containing

Basic information

Region (hg38): 1:119794017-119811580

Links

ENSG00000134193 ∙ NCBI:83998 ∙ OMIM:609846 ∙ HGNC:22977 ∙ Uniprot:Q9BYZ8 ∙ 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 REG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REG4 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			7	1	1	9
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	1	1

Variants in REG4

This is a list of pathogenic ClinVar variants found in the REG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-119794649-C-T		not specified	Uncertain significance (Jul 27, 2021)
1-119794650-G-A		not specified	Uncertain significance (Nov 28, 2024)
1-119794654-G-C		not specified	Uncertain significance (Jun 02, 2023)
1-119798502-T-C		not specified	Uncertain significance (Jan 31, 2023)
1-119798503-T-G			Benign (May 18, 2018)
1-119798535-C-A		not specified	Uncertain significance (Mar 28, 2023)
1-119798580-T-C		not specified	Uncertain significance (May 29, 2024)
1-119799756-G-A		not specified	Uncertain significance (Dec 12, 2023)
1-119799831-T-C		not specified	Uncertain significance (Sep 27, 2024)
1-119803126-T-C		not specified	Uncertain significance (Mar 29, 2023)
1-119803157-T-C		not specified	Uncertain significance (Dec 14, 2023)
1-119808750-C-T		not specified	Uncertain significance (Jun 07, 2024)
1-119808751-G-A		not specified	Likely benign (Aug 08, 2023)
1-119808760-T-C		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REG4	protein_coding	protein_coding	ENST00000354219	5	17643

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000753	0.781	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00289	87	87.1	0.999	0.00000463	1043
Missense in Polyphen		23	27.34	0.84127		344
Synonymous	-0.246	35	33.2	1.05	0.00000197	273
Loss of Function	1.04	6	9.44	0.636	4.02e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.000362	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-independent lectin displaying mannose-binding specificity and able to maintain carbohydrate recognition activity in an acidic environment. May be involved in inflammatory and metaplastic responses of the gastrointestinal epithelium. {ECO:0000269|PubMed:12819006, ECO:0000269|PubMed:20692269}.
• Pathway: Gastric cancer - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.668
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.07

Haploinsufficiency Scores

• pHI: 0.0830
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.102

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Reg4

Gene ontology

• Biological process: response to bacterium
• Cellular component: extracellular region;cytoplasm
• Molecular function: transmembrane signaling receptor activity;calcium ion binding;heparin binding;mannan binding