RITA1

RBPJ interacting and tubulin associated 1

Basic information

Region (hg38): 12:113185526-113192368

Previous symbols: [ "C12orf52" ]

Links

ENSG00000139405 ∙ NCBI:84934 ∙ ∙ HGNC:25925 ∙ Uniprot:Q96K30 ∙ 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 RITA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RITA1 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		1
missense			14	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	0

Variants in RITA1

This is a list of pathogenic ClinVar variants found in the RITA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-113186791-C-T			Likely benign (Jun 01, 2022)
12-113186822-C-T		not specified	Uncertain significance (Mar 30, 2024)
12-113186863-T-G		not specified	Uncertain significance (Mar 06, 2025)
12-113186886-C-G		not specified	Uncertain significance (Feb 08, 2025)
12-113186963-G-C		not specified	Uncertain significance (Mar 20, 2024)
12-113187012-C-T		not specified	Uncertain significance (May 24, 2024)
12-113187014-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-113187020-C-G		not specified	Uncertain significance (Aug 17, 2021)
12-113191360-G-A		not specified	Uncertain significance (Dec 19, 2022)
12-113191381-G-C		not specified	Uncertain significance (Sep 27, 2024)
12-113191419-C-T		not specified	Uncertain significance (Feb 06, 2025)
12-113191435-C-T		not specified	Uncertain significance (Mar 30, 2024)
12-113191446-A-G		not specified	Uncertain significance (Jan 04, 2022)
12-113191465-C-T		not specified	Uncertain significance (Dec 16, 2023)
12-113191500-C-T		not specified	Uncertain significance (May 27, 2022)
12-113191542-G-A		not specified	Uncertain significance (Jun 24, 2022)
12-113191560-A-G		not specified	Likely benign (Nov 26, 2024)
12-113191657-C-G		not specified	Uncertain significance (Dec 20, 2023)
12-113191753-T-G		not specified	Uncertain significance (Aug 14, 2024)
12-113191774-G-A		not specified	Likely benign (Jan 29, 2024)
12-113191777-G-A		not specified	Likely benign (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RITA1	protein_coding	protein_coding	ENST00000548278	2	6843

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00380	0.655	125543	0	197	125740	0.000784

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.445	157	174	0.905	0.0000110	1674
Missense in Polyphen		42	43.142	0.97353		464
Synonymous	1.28	62	76.2	0.814	0.00000484	626
Loss of Function	0.564	4	5.42	0.738	3.98e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000968	0.000965
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.00258	0.00245
Finnish	0.000254	0.000231
European (Non-Finnish)	0.00105	0.000950
Middle Eastern	0.00258	0.00245
South Asian	0.000197	0.000196
Other	0.000557	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tubulin-binding protein that acts as a negative regulator of Notch signaling pathway. Shuttles between the cytoplasm and the nucleus and mediates the nuclear export of RBPJ/RBPSUH, thereby preventing the interaction between RBPJ/RBPSUH and NICD product of Notch proteins (Notch intracellular domain), leading to down-regulate Notch-mediated transcription. May play a role in neurogenesis. {ECO:0000269|PubMed:21102556}.

Intolerance Scores

• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.38

Haploinsufficiency Scores

• pHI: 0.0466
• hipred: N
• hipred_score: 0.123
• ghis: 0.516

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rita1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;Notch signaling pathway;neurogenesis;negative regulation of Notch signaling pathway;nuclear export
• Cellular component: nucleus;cytoplasm;centrosome
• Molecular function: protein binding;tubulin binding