RCC2

regulator of chromosome condensation 2

Basic information

Region (hg38): 1:17406759-17439677

Links

ENSG00000179051 ∙ NCBI:55920 ∙ OMIM:609587 ∙ HGNC:30297 ∙ Uniprot:Q9P258 ∙ 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 RCC2 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCC2 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in RCC2

This is a list of pathogenic ClinVar variants found in the RCC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-17409147-A-T		not specified	Uncertain significance (Dec 18, 2023)
1-17413566-T-C		not specified	Uncertain significance (Apr 12, 2022)
1-17413696-G-C		not specified	Uncertain significance (Aug 08, 2023)
1-17416566-T-C		not specified	Uncertain significance (Nov 27, 2023)
1-17416577-C-T		not specified	Uncertain significance (Nov 06, 2023)
1-17420746-T-C		not specified	Uncertain significance (Dec 07, 2021)
1-17420791-C-G		Malignant tumor of prostate	Uncertain significance (-)
1-17425613-G-A		not specified	Uncertain significance (Sep 07, 2022)
1-17425618-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-17425679-A-G		not specified	Uncertain significance (Jan 19, 2022)
1-17429142-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-17438276-C-T		not specified	Uncertain significance (Feb 06, 2023)
1-17438277-C-A		not specified	Uncertain significance (Dec 27, 2022)
1-17438319-C-A		not specified	Uncertain significance (May 05, 2023)
1-17438391-A-T		not specified	Uncertain significance (Dec 22, 2023)
1-17438419-C-T			Likely benign (Sep 01, 2022)
1-17438423-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-17438469-A-C		not specified	Uncertain significance (Nov 29, 2021)
1-17438484-A-G		not specified	Uncertain significance (Mar 29, 2023)
1-17438495-G-C		not specified	Uncertain significance (Nov 09, 2023)
1-17438498-G-A		not specified	Uncertain significance (Mar 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCC2	protein_coding	protein_coding	ENST00000375436	12	32965

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.956	0.0443	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.09	139	286	0.486	0.0000171	3331
Missense in Polyphen		24	84.188	0.28508		924
Synonymous	-0.664	123	114	1.08	0.00000721	1037
Loss of Function	4.14	4	27.4	0.146	0.00000149	299

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000551	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Multifunctional protein that may effect its functions by regulating the activity of small GTPases, such as RAC1 and RALA (PubMed:12919680, PubMed:25074804, PubMed:26158537, PubMed:28869598). Required for normal progress through the cell cycle, both during interphase and during mitosis (PubMed:23388455, PubMed:12919680, PubMed:26158537). Required for the presence of normal levels of MAD2L1, AURKB and BIRC5 on inner centromeres during mitosis, and for normal attachment of kinetochores to mitotic spindles (PubMed:12919680, PubMed:26158537). Required for normal organization of the microtubule cytoskeleton in interphase cells (PubMed:23388455). Functions as guanine nucleotide exchange factor (GEF) for RALA (PubMed:26158537). Interferes with the activation of RAC1 by guanine nucleotide exchange factors (PubMed:25074804). Prevents accumulation of active, GTP-bound RAC1, and suppresses RAC1-mediated reorganization of the actin cytoskeleton and formation of membrane protrusions (PubMed:25074804, PubMed:28869598). Required for normal cellular responses to contacts with the extracellular matrix of adjacent cells, and for directional cell migration in response to a fibronectin gradient (in vitro) (PubMed:25074804, PubMed:28869598). {ECO:0000269|PubMed:12919680, ECO:0000269|PubMed:23388455, ECO:0000269|PubMed:25074804, ECO:0000269|PubMed:26158537, ECO:0000269|PubMed:28869598}.
• Pathway: Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Intolerance Scores

• loftool: 0.225
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.503
• hipred: Y
• hipred_score: 0.800
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.644

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcc2
• 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); homeostasis/metabolism phenotype; vision/eye phenotype; hematopoietic system phenotype; pigmentation 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)

Zebrafish Information Network

• Gene name: rcc2
• Affected structure: pharyngeal arch 1
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: cell cycle;integrin-mediated signaling pathway;regulation of fibroblast migration;positive regulation of G2/M transition of mitotic cell cycle;regulation of cell migration;negative regulation of GTPase activity;establishment of protein localization;focal adhesion assembly;cell division;negative regulation of focal adhesion assembly;positive regulation of attachment of spindle microtubules to kinetochore;chromosome passenger complex localization to kinetochore;activation of GTPase activity;negative regulation of substrate adhesion-dependent cell spreading;regulation of ruffle assembly
• Cellular component: nucleolus;cytosol;microtubule;plasma membrane;membrane;midbody;early endosome membrane;chromosome, centromeric core domain;mitotic spindle midzone
• Molecular function: RNA binding;guanyl-nucleotide exchange factor activity;protein binding;microtubule binding;protein kinase binding;protein domain specific binding;small GTPase binding;Rac GTPase binding