RCC1

protein-coding

regulator of chromosome condensation 1

Gene summary

Enables several functions, including guanyl-nucleotide exchange factor activity; nucleosomal DNA binding activity; and protein heterodimerization activity. Involved in G1/S transition of mitotic cell cycle; regulation of cell cycle process; and spindle organization. Located in chromatin; cytoplasm; and nuclear lumen. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CHC1

MANE transcript

NM_001381865.2

Inheritance

—

ClinVar variants

P:10U:43B:2

Top phenotype

Infection-induced acute-onset axonal neuropathy

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr1:28,505,943-28,539,300

External References & Databases

Ensembl (ENSG00000180198)

Transcript & Mutation Effects

hg38 • Region Span ~33.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RCC1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 45

Infection-induced acute-onset axonal neuropathyTotal: 11

See casesTotal: 7

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001381865.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense	2 clinvar	8 clinvar	41 clinvar	2 clinvar		53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	2	8	43	2	0	55

Highest pathogenic variant AF is 0.00003717541

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 124 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001381865.2	RefSeq	NP_001368794.1	9	MANE Select
ENST00000683442.1	Ensembl	ENSP00000508074.1	9	MANE Select
NM_001048194.4	RefSeq	NP_001041659.1	10	Standard
NM_001048195.4	RefSeq	NP_001041660.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

G1/S transition of mitotic cell cycle
mitotic spindle organization
chromosome segregation
regulation of mitotic nuclear division
viral process

Molecular Function

chromatin binding
Ran guanyl-nucleotide exchange factor activity
protein binding
Ran GTPase binding
nucleosome binding

Cellular Component

chromatin
nuclear chromatin
condensed nuclear chromosome
nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373831
Coding exons: 10
Length: 33358
Individuals with no LoFs: 124495
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 124498
p: 0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.68	201	280	0.717	0.0000168	2910
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.371

Intolerance Scores

LoFtool: 0.121
RVIS EVS: -0.56
RVIS percentile EVS: 19.54

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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