RGN

regucalcin

Basic information

Region (hg38): X:47078355-47093314

Links

ENSG00000130988 ∙ NCBI:9104 ∙ OMIM:300212 ∙ HGNC:9989 ∙ Uniprot:Q15493 ∙ 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 RGN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGN 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
missense			33		1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	33	1	2

Variants in RGN

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

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

Position	Type	Phenotype	Significance	ClinVar
X-47081187-C-T		not specified	Uncertain significance (Jul 20, 2021)
X-47081266-G-A		not specified	Uncertain significance (Apr 18, 2024)
X-47081296-G-A		not specified	Uncertain significance (Apr 07, 2022)
X-47084435-G-A		not specified	Uncertain significance (Dec 16, 2024)
X-47084435-G-C		not specified	Uncertain significance (Aug 03, 2022)
X-47084445-G-T		not specified	Uncertain significance (Apr 08, 2024)
X-47084448-A-C		not specified	Uncertain significance (Dec 28, 2022)
X-47084472-T-C		not specified	Uncertain significance (May 26, 2024)
X-47084555-C-T			Benign (Sep 19, 2018)
X-47084562-A-G		not specified	Uncertain significance (Mar 21, 2023)
X-47084584-C-T			Likely benign (Nov 01, 2022)
X-47084585-G-A		not specified	Uncertain significance (Apr 08, 2022)
X-47084598-C-G		not specified	Uncertain significance (Feb 22, 2023)
X-47084610-C-T			Benign (Jan 25, 2018)
X-47089778-A-G		not specified	Uncertain significance (Jan 29, 2024)
X-47089791-A-G		not specified	Uncertain significance (May 28, 2024)
X-47089812-A-G		not specified	Uncertain significance (May 18, 2023)
X-47089814-C-T		not specified	Uncertain significance (Nov 24, 2024)
X-47089815-G-A		not specified	Uncertain significance (Jan 02, 2025)
X-47089833-A-T		not specified	Uncertain significance (May 18, 2023)
X-47089835-T-C		not specified	Uncertain significance (May 29, 2024)
X-47089838-C-G		not specified	Uncertain significance (Jan 14, 2025)
X-47089855-C-A		not specified	Uncertain significance (Nov 23, 2024)
X-47089863-A-G		not specified	Uncertain significance (Mar 05, 2024)
X-47089872-A-T		not specified	Uncertain significance (Jan 23, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGN	protein_coding	protein_coding	ENST00000397180	6	14938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0221	0.916	125711	12	21	125744	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.913	138	111	1.24	0.00000868	1939
Missense in Polyphen		43	37.541	1.1454		642
Synonymous	0.190	41	42.6	0.963	0.00000344	578
Loss of Function	1.60	4	9.23	0.433	6.54e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000306
Ashkenazi Jewish	0.000808	0.000595
East Asian	0.000146	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000164	0.000114
Middle Eastern	0.000146	0.000109
South Asian	0.000267	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Gluconolactonase with low activity towards other sugar lactones, including gulonolactone and galactonolactone. Can also hydrolyze diisopropyl phosphorofluoridate and phenylacetate (in vitro). Calcium-binding protein. Modulates Ca(2+) signaling, and Ca(2+)-dependent cellular processes and enzyme activities (By similarity). {ECO:0000250}.
• Pathway: Ascorbate and aldarate metabolism - Homo sapiens (human);Pentose phosphate pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.344

Intolerance Scores

• loftool: 0.396
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.398
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rgn
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); 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); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; vision/eye phenotype; cellular phenotype; skeleton phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: kidney development;negative regulation of protein kinase activity;cellular calcium ion homeostasis;spermatogenesis;aging;positive regulation of triglyceride biosynthetic process;positive regulation of glucose metabolic process;positive regulation of phosphatase activity;L-ascorbic acid biosynthetic process;negative regulation of phosphoprotein phosphatase activity;positive regulation of ATPase activity;negative regulation of GTPase activity;negative regulation of apoptotic process;positive regulation of GTPase activity;negative regulation of nitric oxide biosynthetic process;positive regulation of fatty acid biosynthetic process;negative regulation of epithelial cell proliferation;regulation of calcium-mediated signaling;negative regulation of cyclic-nucleotide phosphodiesterase activity;liver regeneration;negative regulation of flagellated sperm motility;positive regulation of superoxide dismutase activity;positive regulation of calcium-transporting ATPase activity;negative regulation of RNA biosynthetic process;negative regulation of bone development;positive regulation of proteolysis involved in cellular protein catabolic process;negative regulation of calcium-dependent ATPase activity;negative regulation of DNA catabolic process;positive regulation of dUTP diphosphatase activity;negative regulation of leucine-tRNA ligase activity;negative regulation of DNA biosynthetic process
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: gluconolactonase activity;calcium ion binding;zinc ion binding;enzyme regulator activity