RCBTB2

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

Basic information

Region (hg38): 13:48488963-48533256

Previous symbols: [ "CHC1L" ]

Links

ENSG00000136161 ∙ NCBI:1102 ∙ OMIM:603524 ∙ HGNC:1914 ∙ Uniprot:O95199 ∙ 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 RCBTB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCBTB2 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			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	0

Variants in RCBTB2

This is a list of pathogenic ClinVar variants found in the RCBTB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-48490187-C-T		not specified	Uncertain significance (Dec 02, 2022)
13-48490202-A-T		not specified	Uncertain significance (Jun 22, 2023)
13-48496226-C-T		not specified	Uncertain significance (Jan 03, 2024)
13-48496249-C-G		not specified	Uncertain significance (Aug 30, 2022)
13-48499627-C-T		not specified	Uncertain significance (Jun 30, 2022)
13-48499660-A-G		not specified	Uncertain significance (Apr 13, 2022)
13-48499669-C-T		not specified	Uncertain significance (Jul 14, 2023)
13-48499681-G-A		not specified	Uncertain significance (Mar 28, 2023)
13-48499690-G-C		not specified	Uncertain significance (Jan 18, 2022)
13-48499743-G-A		not specified	Uncertain significance (Jul 14, 2022)
13-48499746-C-T		not specified	Uncertain significance (Aug 09, 2021)
13-48499747-G-A		not specified	Uncertain significance (Jun 07, 2024)
13-48501784-T-A		not specified	Uncertain significance (May 24, 2024)
13-48501838-G-A		not specified	Uncertain significance (Sep 28, 2022)
13-48502748-C-T		not specified	Uncertain significance (Aug 23, 2021)
13-48502756-G-A		not specified	Uncertain significance (Sep 17, 2021)
13-48502775-C-T		not specified	Uncertain significance (Jan 23, 2024)
13-48502779-G-C		not specified	Uncertain significance (Aug 12, 2021)
13-48502828-C-T		not specified	Uncertain significance (Nov 10, 2022)
13-48510633-C-T		not specified	Uncertain significance (Feb 06, 2024)
13-48510666-G-T		not specified	Uncertain significance (Jan 13, 2023)
13-48510708-C-T		not specified	Uncertain significance (May 21, 2024)
13-48510710-C-G		not specified	Uncertain significance (Jul 25, 2023)
13-48511778-C-T		not specified	Uncertain significance (Aug 08, 2023)
13-48512046-C-T		not specified	Uncertain significance (May 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCBTB2	protein_coding	protein_coding	ENST00000344532	12	44275

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.49e-9	0.894	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0584	313	310	1.01	0.0000169	3587
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000593	0.000592
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000490	0.000489
South Asian	0.000375	0.000359
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0890

Intolerance Scores

• loftool: 0.410
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.8

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.352
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.279

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcbtb2

Gene ontology

• Cellular component: acrosomal vesicle
• Molecular function: Ran guanyl-nucleotide exchange factor activity;protein binding