RFC1 replication factor C subunit 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RFC1provided by HGNC
Official Full Name: replication factor C subunit 1provided by HGNC
Primary source: HGNC:HGNC:9969
See related: Ensembl:ENSG00000035928 MIM:102579; AllianceGenome:HGNC:9969
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: A1; RFC; PO-GA; RECC1; CANVAS; MHCBFB; RFC140
Summary: This gene encodes the large subunit of replication factor C, a five subunit DNA polymerase accessory protein, which is a DNA-dependent ATPase required for eukaryotic DNA replication and repair. The large subunit acts as an activator of DNA polymerases, binds to the 3' end of primers, and promotes coordinated synthesis of both strands. It may also have a role in telomere stability. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2011]
Annotation information: Note: RFC1 (GeneID: 5981) and SLC19A1 (GeneID: 6573) share the RFC1 symbol/alias in common. RFC1 is the official symbol for the gene name 'replication factor C subunit 1' and is an alias for 'reduced folate carrier 1' on the 'solute carrier family 19 member 1' gene. [18 May 2018]
Expression: Ubiquitous expression in lymph node (RPKM 16.8), thyroid (RPKM 15.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4p14

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (39287456..39366362, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (39257079..39354488, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (39289076..39367982, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Structural polymorphism of the nucleic acids in pentanucleotide repeats associated with the neurological disorder CANVAS.
Title: Structural polymorphism of the nucleic acids in pentanucleotide repeats associated with the neurological disorder CANVAS.
[Late-Onset Cerebellar Ataxia with Neuropathy: Uncovering the Role of RFC1 Gene Mutations].
Title: [Late-Onset Cerebellar Ataxia with Neuropathy: Uncovering the Role of RFC1 Gene Mutations].
RNA Foci in Two bi-Allelic RFC1 Expansion Carriers.
Title: RNA Foci in Two bi-Allelic RFC1 Expansion Carriers.
Investigation of RFC1 tandem nucleotide repeat locus in diverse neurodegenerative outcomes in an Indian cohort.
Title: Investigation of RFC1 tandem nucleotide repeat locus in diverse neurodegenerative outcomes in an Indian cohort.
Cranial Nerve Thinning Distinguishes RFC1-Related Disorder from Other Late-Onset Ataxias.
Title: Cranial Nerve Thinning Distinguishes RFC1-Related Disorder from Other Late-Onset Ataxias.
Can CANVAS due to RFC1 biallelic expansions present with pure ataxia?
Title: Can CANVAS due to RFC1 biallelic expansions present with pure ataxia?
Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis.
Title: Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis.
CANVAS-related RFC1 mutations in patients with immune-mediated neuropathy.
Title: CANVAS-related RFC1 mutations in patients with immune-mediated neuropathy.
Frequency and Phenotype of RFC1 Repeat Expansions in Bilateral Vestibulopathy.
Title: Frequency and Phenotype of RFC1 Repeat Expansions in Bilateral Vestibulopathy.
Shaking Up Ataxia: FGF14 and RFC1 Repeat Expansions in Affected and Unaffected Members of a Chilean Family.
Title: Shaking Up Ataxia: FGF14 and RFC1 Repeat Expansions in Affected and Unaffected Members of a Chilean Family.

Submit: New GeneRIF Correction See all GeneRIFs (51)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome MedGen: C3281223 OMIM: 614575 GeneReviews: Hereditary Ataxia Overview, RFC1 CANVAS / Spectrum Disorder	Compare labs

EBI GWAS Catalog

Description
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat interacts with the RNA polymerase II holoenzyme, which includes RFC, during Tat-mediated transactivation of the HIV-1 LTR	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D4S2821 (e-PCR)
- UniSTS:52763

SHGC-67924 (e-PCR)
- UniSTS:18746

SHGC-30256 (e-PCR)
- UniSTS:52560

D4S335 (e-PCR)
- UniSTS:27992

G34472 (e-PCR)
- UniSTS:9917

SHGC-67941 (e-PCR)
- UniSTS:16318

G67564 (e-PCR)
- UniSTS:207040

G62134 (e-PCR)
- UniSTS:139201

G67567 (e-PCR)
- UniSTS:207041

G67568 (e-PCR)
- UniSTS:207042

G67569 (e-PCR)
- UniSTS:207043

G67570 (e-PCR)
- UniSTS:207044

G67571 (e-PCR)
- UniSTS:207045

G67565 (e-PCR)
- UniSTS:207046

D4S2578E (e-PCR)
- UniSTS:150982

G67566 (e-PCR)
- UniSTS:207047

SHGC-51647 (e-PCR)
- UniSTS:69086

STS-Z22642 (e-PCR)
- UniSTS:80101

STS-L23320 (e-PCR)
- UniSTS:30696

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp unloader activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA clamp unloader activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor binding	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables enzyme activator activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA clamp unloading	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated DNA replication	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in telomere maintenance via telomerase	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of DNA replication factor C complex	IDA Inferred from Direct Assay more info	PubMed
part_of DNA replication factor C complex	IPI Inferred from Physical Interaction more info	PubMed
part_of Elg1 RFC-like complex	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: replication factor C subunit 1

Names: A1 140 kDa subunit; DNA-binding protein PO-GA; MHC binding factor, beta; RF-C 140 kDa subunit; activator 1 140 kDa subunit; activator 1 large subunit; activator 1 subunit 1; replication factor C (activator 1) 1, 145kDa; replication factor C 140 kDa subunit; replication factor C large subunit; replication factor C1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001204747.2 → NP_001191676.1 replication factor C subunit 1 isoform 2

See identical proteins and their annotated locations for NP_001191676.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site at an internal coding exon compared to variant 1, resulting in an isoform (2) that is 1 aa longer than isoform 1.

Source sequence(s)

AK291612, BC035297, BC051751, DA336360

Consensus CDS

CCDS56329.1

UniProtKB/Swiss-Prot

A8K6E7, P35251, Q5XKF5, Q6PKU0, Q86V41, Q86V46

Related

ENSP00000371321.1, ENST00000381897.5

Conserved Domains (5) summary

COG5275
Location:272 → 502

COG5275; BRCT domain type II [General function prediction only]

pfam08519
Location:915 → 1067

RFC1; Replication factor RFC1 C terminal domain

cl25701
Location:584 → 1003

RuvB_N; Holliday junction DNA helicase ruvB N-terminus

cl26511
Location:14 → 404

Neuromodulin_N; Gap junction protein N-terminal region

cl27300
Location:392 → 479

LIGANc; NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction ...
NM_001363495.2 → NP_001350424.1 replication factor C subunit 1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) has lacks an alternate, in-frame exon in the coding region compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.

Source sequence(s)

AC023135, AC093855

Conserved Domains (5) summary

COG5275
Location:246 → 476

COG5275; BRCT domain type II [General function prediction only]

pfam08519
Location:888 → 1040

RFC1; Replication factor RFC1 C terminal domain

cl25701
Location:558 → 976

RuvB_N; Holliday junction DNA helicase ruvB N-terminus

cl26511
Location:14 → 378

Neuromodulin_N; Gap junction protein N-terminal region

cl27300
Location:366 → 453

LIGANc; NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction ...
NM_001363496.2 → NP_001350425.1 replication factor C subunit 1 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) has multiple differences in the coding region compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.

Source sequence(s)

AC023135, AC093855

Conserved Domains (5) summary

COG5275
Location:246 → 476

COG5275; BRCT domain type II [General function prediction only]

pfam08519
Location:889 → 1041

RFC1; Replication factor RFC1 C terminal domain

cl25701
Location:558 → 977

RuvB_N; Holliday junction DNA helicase ruvB N-terminus

cl26511
Location:14 → 378

Neuromodulin_N; Gap junction protein N-terminal region

cl27300
Location:366 → 453

LIGANc; NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction ...
NM_002913.5 → NP_002904.3 replication factor C subunit 1 isoform 1

See identical proteins and their annotated locations for NP_002904.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript, and encodes isoform 1.

Source sequence(s)

BC035297, BC051751, DA336360

Consensus CDS

CCDS3450.1

UniProtKB/Swiss-Prot

P35251

Related

ENSP00000261424.4, ENST00000349703.7

Conserved Domains (4) summary

smart00382
Location:647 → 777

AAA; ATPases associated with a variety of cellular activities

cd00027
Location:409 → 480

BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...

pfam00004
Location:647 → 775

AAA; ATPase family associated with various cellular activities (AAA)

pfam08519
Location:914 → 1067

RFC1; Replication factor RFC1 C terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

39287456..39366362 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416054.1 → XP_047272010.1 replication factor C subunit 1 isoform X2
XM_011513731.2 → XP_011512033.1 replication factor C subunit 1 isoform X1

Conserved Domains (3) summary

cd00027
Location:409 → 480

BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...

pfam08519
Location:745 → 898

RFC1; Replication factor RFC1 C terminal domain

cl21455
Location:497 → 606

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases