RCC1

regulator of chromosome condensation 1

Basic information

Region (hg38): 1:28505943-28539300

Previous symbols: [ "CHC1" ]

Links

ENSG00000180198 ∙ NCBI:1104 ∙ OMIM:179710 ∙ HGNC:1913 ∙ Uniprot:P18754 ∙ 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 RCC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCC1 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in RCC1

This is a list of pathogenic ClinVar variants found in the RCC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-28529879-C-A		not specified	Uncertain significance (Mar 22, 2023)
1-28529879-C-T		not specified	Uncertain significance (Oct 29, 2021)
1-28529880-G-A		not specified	Uncertain significance (Mar 19, 2024)
1-28530600-C-A		not specified	Uncertain significance (Apr 12, 2024)
1-28530606-A-C		not specified	Uncertain significance (Sep 16, 2021)
1-28530610-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-28531856-G-A		See cases	Pathogenic (Jan 11, 2024)
1-28531859-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-28531967-G-A		See cases	Likely pathogenic (Jan 11, 2024)
1-28532189-A-G		See cases	Likely pathogenic (Jan 11, 2024)
1-28532215-C-A		not specified	Uncertain significance (Feb 22, 2023)
1-28532239-G-C		See cases	Likely pathogenic (Jan 11, 2024)
1-28532325-G-A		See cases	Uncertain significance (Jan 11, 2024)
1-28532327-G-A		not specified	Uncertain significance (Sep 21, 2023)
1-28535054-A-G		not specified	Uncertain significance (Sep 22, 2022)
1-28535263-G-A		not specified	Uncertain significance (May 24, 2023)
1-28535323-G-A		See cases	Likely pathogenic (Jan 11, 2024)
1-28535958-A-G		not specified	Uncertain significance (Feb 28, 2023)
1-28536268-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-28536278-A-C		not specified	Uncertain significance (Dec 06, 2022)
1-28536322-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-28536747-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-28536855-C-T		not specified	Uncertain significance (May 24, 2023)
1-28536863-T-A		not specified	Uncertain significance (Mar 27, 2023)
1-28537887-T-A		not specified	Likely benign (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCC1	protein_coding	protein_coding	ENST00000373831	10	33358

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.931	0.0689	124495	0	3	124498	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.68	201	280	0.717	0.0000168	2910
Missense in Polyphen		42	79.063	0.53122		766
Synonymous	0.390	110	115	0.954	0.00000723	936
Loss of Function	3.72	3	21.7	0.138	0.00000111	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine-nucleotide releasing factor that promotes the exchange of Ran-bound GDP by GTP, and thereby plays an important role in RAN-mediated functions in nuclear import and mitosis (PubMed:1944575, PubMed:17435751, PubMed:20668449, PubMed:22215983, PubMed:11336674). Contributes to the generation of high levels of chromosome-associated, GTP-bound RAN, which is important for mitotic spindle assembly and normal progress through mitosis (PubMed:12194828, PubMed:17435751, PubMed:22215983). Via its role in maintaining high levels of GTP-bound RAN in the nucleus, contributes to the release of cargo proteins from importins after nuclear import (PubMed:22215983). Involved in the regulation of onset of chromosome condensation in the S phase (PubMed:3678831). Binds both to the nucleosomes and double- stranded DNA (PubMed:17435751, PubMed:18762580). {ECO:0000269|PubMed:11336674, ECO:0000269|PubMed:12194828, ECO:0000269|PubMed:17435751, ECO:0000269|PubMed:18762580, ECO:0000269|PubMed:1944575, ECO:0000269|PubMed:20668449, ECO:0000269|PubMed:22215983, ECO:0000269|PubMed:3678831}.
• Pathway: Disease;role of ran in mitotic spindle regulation;cycling of ran in nucleocytoplasmic transport;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;Infectious disease;mechanism of protein import into the nucleus;Nuclear import of Rev protein;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.371

Intolerance Scores

• loftool: 0.121
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.736
• ghis: 0.612

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcc1

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;mitotic spindle organization;chromosome segregation;regulation of mitotic nuclear division;viral process;spindle assembly;protein heterotetramerization;cell division
• Cellular component: chromatin;nuclear chromatin;condensed nuclear chromosome;nucleus;nucleoplasm;cytoplasm;nuclear membrane;protein-containing complex
• Molecular function: chromatin binding;Ran guanyl-nucleotide exchange factor activity;protein binding;Ran GTPase binding;nucleosome binding;nucleosomal DNA binding;histone binding;sulfate binding;protein heterodimerization activity