RCC1L

protein-coding

RCC1 like

Gene summary

This gene encodes a protein containing regulator of chromosome condensation 1-like repeats. The encoded protein may function as a guanine nucleotide exchange factor. This gene is located in a region of chromosome 7 that is deleted in Williams-Beuren syndrome, a multisystem developmental disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

Previous symbols:

WBSCR16

MANE transcript

NM_030798.5

Inheritance

—

ClinVar variants

U:9B:1

Top phenotype

—

Max pathogenic AF

—

Genomic locus

chr7:75,027,122-75,074,228

External References & Databases

Ensembl (ENSG00000274523)

Transcript & Mutation Effects

hg38 • Region Span ~47.1 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 RCC1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 5

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030798.5. 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			7 clinvar		1 clinvar	8
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	9	0	1	10

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 48 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030798.5	RefSeq	NP_110425.2	11	MANE Select
ENST00000610322.5	Ensembl	ENSP00000480364.1	11	MANE Select
NM_001281441.2	RefSeq	NP_001268370.1	9	Standard
NM_001363447.2	RefSeq	NP_001350376.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of mitochondrial translation
mitochondrial membrane fusion

Molecular Function

RNA binding
guanyl-nucleotide exchange factor activity
protein binding
GTP binding
rRNA binding

Cellular Component

mitochondrial inner membrane
mitochondrial membrane

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Guanine nucleotide exchange factor (GEF) for mitochondrial dynamin-related GTPase OPA1. Activates OPA1, by exchanging bound GDP for free GTP, and drives OPA1 and MFN1- dependent mitochondrial fusion (PubMed:28746876). Plays an essential role in mitochondrial ribosome biogenesis. As a component of a functional protein-RNA module, consisting of RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2 and 16S mitochondrial ribosomal RNA (16S mt-rRNA), controls 16S mt-rRNA abundance and is required for intra-mitochondrial translation of core subunits of the oxidative phosphorylation system (PubMed:27667664). {ECO:0000269|PubMed:27667664, ECO:0000269|PubMed:28746876}.;
Disease: DISEASE: Note=WBSCR16 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of WBSCR16 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease. {ECO:0000305|PubMed:12073013}.;

Recessive Scores

pRec: 0.0816