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
• exudative vitreoretinopathy (Limited), mode of inheritance: AD

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 (341 variants)
• not_specified (63 variants)
• Retinal_dystrophy (9 variants)
• RCBTB1-related_disorder (8 variants)
• RCBTB1-related_retinopathy (6 variants)
• Retinitis_pigmentosa (6 variants)
• Exudative_retinopathy (2 variants)
• RETINAL_DYSTROPHY_WITH_EXTRAOCULAR_ANOMALIES (2 variants)
• Familial_exudative_vitreoretinopathy (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. These statistics are base on transcript: NM_000018191.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	84	6	92
missense	1	4	171	3	1	180
nonsense	9		1			10
start loss						0
frameshift	8	3	1			12
splice donor/acceptor (+/-2bp)		8		1		9
Total	18	15	175	88	7

Highest pathogenic variant AF is 0.0000935602

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