RCBTB1

RCC1 and BTB domain containing protein 1, the group of BTB domain containing

Basic information

Region (hg38): 13:49531946-49585558

Links

ENSG00000136144 ∙ NCBI:55213 ∙ OMIM:607867 ∙ HGNC:18243 ∙ Uniprot:Q8NDN9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• RCBTB1-related retinopathy (Limited), mode of inheritance: AR
• reticular dystrophy of the retinal pigment epithelium (Supportive), mode of inheritance: AR
• exudative vitreoretinopathy (Limited), mode of inheritance: AD
• RCBTB1-related retinopathy (Limited), mode of inheritance: AR
• RCBTB1-related retinopathy (Strong), mode of inheritance: AR
• RCBTB1-related retinopathy (Strong), mode of inheritance: AR
• RCBTB1-related retinopathy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinal dystrophy with or without extraocular anomalies (RDEOA)	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	27486781

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RCBTB1 gene.

• not provided (17 variants)
• RCBTB1-related retinopathy (1 variants)
• Exudative retinopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCBTB1 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			1	76	14	91
missense	1	1	149	3	2	156
nonsense	7		1			8
start loss						0
frameshift	9	1	1			11
inframe indel			3			3
splice donor/acceptor (+/-2bp)		4		1		5
splice region			8	10	2	20
non coding				39	32	71
Total	17	6	155	119	48

Highest pathogenic variant AF is 0.0000920

Variants in RCBTB1

This is a list of pathogenic ClinVar variants found in the RCBTB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-49534116-T-C		RCBTB1-related retinopathy	Benign (Nov 07, 2021)
13-49534118-C-T		RCBTB1-related disorder	Benign (Sep 13, 2019)
13-49534125-G-C			Uncertain significance (Jun 10, 2022)
13-49534134-G-C			Likely benign (Jan 02, 2024)
13-49534150-G-C			Uncertain significance (Feb 18, 2022)
13-49534164-T-A			Uncertain significance (Mar 19, 2022)
13-49534175-G-C			Uncertain significance (Sep 27, 2019)
13-49534178-G-A			Uncertain significance (Oct 01, 2021)
13-49534180-C-G			Uncertain significance (Mar 09, 2023)
13-49534182-A-T			Uncertain significance (Jun 03, 2022)
13-49534191-C-T			Uncertain significance (Feb 08, 2022)
13-49534193-A-C			Uncertain significance (Jul 06, 2022)
13-49534206-C-A			Uncertain significance (Apr 12, 2022)
13-49534214-C-G			Uncertain significance (Feb 11, 2022)
13-49534220-T-A			Uncertain significance (Nov 28, 2022)
13-49534224-A-G			Likely benign (Apr 18, 2023)
13-49534224-ATGAT-A			Uncertain significance (Jun 05, 2022)
13-49534226-G-A			Uncertain significance (Jun 29, 2022)
13-49534228-T-C			Benign (Jan 05, 2024)
13-49534250-A-G			Uncertain significance (Jun 13, 2022)
13-49534261-T-C			Uncertain significance (Sep 01, 2021)
13-49534272-C-G			Likely benign (Apr 06, 2022)
13-49534276-A-G			Likely benign (Aug 21, 2022)
13-49534344-C-G			Benign (May 26, 2021)
13-49540845-T-A			Benign (May 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCBTB1	protein_coding	protein_coding	ENST00000378302	11	53638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000156	0.992	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	245	295	0.831	0.0000159	3455
Missense in Polyphen		57	81.485	0.69951		1008
Synonymous	0.335	115	120	0.961	0.00000743	1032
Loss of Function	2.39	14	27.6	0.508	0.00000137	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000292	0.000292
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000489	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000141	0.000132
Middle Eastern	0.000489	0.000489
South Asian	0.000136	0.000131
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in cell cycle regulation by chromatin remodeling. {ECO:0000269|PubMed:11306461}.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.462
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.78

Haploinsufficiency Scores

• pHI: 0.224
• hipred: N
• hipred_score: 0.394
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.595

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcbtb1

Zebrafish Information Network

• Gene name: rcbtb1
• Affected structure: ocular blood vessel
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: chromatin organization;cell cycle
• Cellular component: nucleus;cytoplasm