RCBTB2

protein-coding

RCC1 and BTB domain containing protein 2, the group of BTB domain containing

Gene summary

This gene encodes a protein containing two C-terminal BTB/POZ domains that is related to regulator of chromosome condensation (RCC). The encoded protein may act as a guanine nucleotide exchange factor. This gene is observed to be lost or underexpressed in prostate cancers. There is a pseudogene of this gene on chromosome 10. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

Previous symbols:

CHC1L

MANE transcript

NM_001268.4

Inheritance

—

ClinVar variants

U:74

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr13:48,488,963-48,533,256

External References & Databases

Ensembl (ENSG00000136161)

Transcript & Mutation Effects

hg38 • Region Span ~44.3 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 RCBTB2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 69

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001268.4. 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			4 clinvar			4
missense			69 clinvar			69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	74	0	0	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001268.4	RefSeq	NP_001259.1	12	MANE Select
ENST00000344532.8	Ensembl	ENSP00000345144.3	12	MANE Select
NM_001286830.2	RefSeq	NP_001273759.1	12	Standard
NM_001286831.2	RefSeq	NP_001273760.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

Ran guanyl-nucleotide exchange factor activity
protein binding

Cellular Component

acrosomal vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344532
Coding exons: 12
Length: 44275
Individuals with no LoFs: 125686
Homozygous LoFs: 0
Heterozygous LoFs: 62
Defined: 125748
p: 0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0584	313	310	1.01	0.0000169	3587
Missense (PolyPhen)		96	100.93	0.95118		1209
Synonymous	0.831	110	122	0.904	0.00000738	1072
Loss of Function	1.79	18	28.2	0.637	0.00000133	341

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.00038	0.00036	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0890

Intolerance Scores

LoFtool: 0.410
RVIS EVS: -0.87
RVIS percentile EVS: 10.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.279

Gene Damage Prediction

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