RCN3

reticulocalbin 3, the group of CREC family

Basic information

Region (hg38): 19:49528003-49546962

Links

ENSG00000142552 ∙ NCBI:57333 ∙ OMIM:619032 ∙ HGNC:21145 ∙ Uniprot:Q96D15 ∙ 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 RCN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCN3 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				2		2
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in RCN3

This is a list of pathogenic ClinVar variants found in the RCN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49528557-C-G		not specified	Uncertain significance (Nov 01, 2022)
19-49528637-C-A		not specified	Uncertain significance (May 14, 2024)
19-49528639-A-G		not specified	Uncertain significance (Jan 27, 2022)
19-49528680-C-A		not specified	Uncertain significance (Jul 09, 2021)
19-49534222-G-A		not specified	Uncertain significance (Apr 15, 2024)
19-49534251-G-A		not specified	Uncertain significance (Oct 10, 2023)
19-49534261-C-T		not specified	Uncertain significance (Sep 26, 2022)
19-49534351-G-C		not specified	Uncertain significance (Apr 13, 2022)
19-49534359-G-A		not specified	Uncertain significance (Mar 25, 2022)
19-49537057-A-G		not specified	Uncertain significance (Aug 30, 2022)
19-49537086-C-T		not specified	Uncertain significance (Mar 28, 2023)
19-49537091-C-T			Likely benign (Oct 01, 2022)
19-49537095-C-T		not specified	Uncertain significance (Mar 21, 2022)
19-49537099-G-A		not specified	Uncertain significance (May 08, 2023)
19-49537138-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-49537146-G-A		not specified	Uncertain significance (Apr 15, 2024)
19-49537147-A-T		not specified	Uncertain significance (Apr 15, 2024)
19-49537170-G-A		not specified	Uncertain significance (May 25, 2022)
19-49537189-G-A		not specified	Uncertain significance (Dec 11, 2023)
19-49539123-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-49542565-C-T		not specified	Uncertain significance (Dec 14, 2023)
19-49542568-C-A		not specified	Uncertain significance (Mar 01, 2024)
19-49542589-C-T		not specified	Uncertain significance (May 28, 2024)
19-49542630-C-T		not specified	Uncertain significance (Aug 20, 2023)
19-49542666-G-A		not specified	Uncertain significance (May 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCN3	protein_coding	protein_coding	ENST00000270645	6	19345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.81e-11	0.0264	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.215	173	181	0.955	0.0000108	2089
Missense in Polyphen		55	54.7	1.0055		605
Synonymous	0.457	70	75.0	0.933	0.00000469	615
Loss of Function	-0.443	15	13.3	1.13	6.94e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000625	0.000600
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000366	0.000352
Middle Eastern	0.000116	0.000109
South Asian	0.000290	0.000261
Other	0.000921	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable molecular chaperone assisting protein biosynthesis and transport in the endoplasmic reticulum (PubMed:16433634, PubMed:28939891). Required for the proper biosynthesis and transport of pulmonary surfactant-associated protein A/SP-A, pulmonary surfactant-associated protein D/SP-D and the lipid transporter ABCA3 (By similarity). By regulating both the proper expression and the degradation through the endoplasmic reticulum-associated protein degradation pathway of these proteins plays a crucial role in pulmonary surfactant homeostasis (By similarity). Has an anti-fibrotic activity by negatively regulating the secretion of type I and type III collagens (PubMed:28939891). This calcium-binding protein also transiently associates with immature PCSK6 and regulates its secretion (PubMed:16433634). {ECO:0000250|UniProtKB:Q8BH97, ECO:0000269|PubMed:16433634, ECO:0000269|PubMed:28939891}.

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.74

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.291
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.792

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcn3

Gene ontology

• Biological process: protein secretion;positive regulation of peptidase activity;protein transport;collagen biosynthetic process;ERAD pathway;surfactant homeostasis;regulation of protein kinase B signaling;phospholipid homeostasis;lung epithelium development
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen
• Molecular function: calcium ion binding;protein binding