CIR1

corepressor interacting with RBPJ, CIR1

Basic information

Region (hg38): 2:174348022-174395712

Links

ENSG00000138433 ∙ NCBI:9541 ∙ OMIM:605228 ∙ HGNC:24217 ∙ Uniprot:Q86X95 ∙ 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 CIR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CIR1 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			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	0

Variants in CIR1

This is a list of pathogenic ClinVar variants found in the CIR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-174348549-A-G		not specified	Uncertain significance (Jun 16, 2024)
2-174348619-G-C		not specified	Uncertain significance (Dec 13, 2023)
2-174348624-C-T		not specified • EBV-positive nodal T- and NK-cell lymphoma	Uncertain significance (Oct 10, 2023)
2-174348633-C-T		not specified	Uncertain significance (Apr 08, 2024)
2-174348634-G-A		not specified	Uncertain significance (Aug 01, 2024)
2-174348678-C-T		not specified	Uncertain significance (Dec 04, 2024)
2-174348687-C-T		not specified	Uncertain significance (Dec 12, 2023)
2-174348688-G-A		not specified	Uncertain significance (Apr 12, 2022)
2-174348742-C-T		not specified	Uncertain significance (May 10, 2023)
2-174348763-T-C		not specified	Uncertain significance (Dec 21, 2023)
2-174348772-T-C		not specified	Uncertain significance (Oct 10, 2023)
2-174348796-G-A		not specified	Uncertain significance (Aug 05, 2024)
2-174348816-C-G		not specified	Uncertain significance (May 31, 2023)
2-174348840-C-T		not specified	Uncertain significance (Nov 08, 2024)
2-174348859-T-C		not specified	Uncertain significance (Sep 25, 2023)
2-174348898-G-A		not specified	Uncertain significance (Jun 07, 2023)
2-174348919-C-A		not specified	Uncertain significance (Dec 20, 2023)
2-174348934-C-T		not specified	Uncertain significance (Apr 19, 2023)
2-174348986-T-A		not specified	Uncertain significance (Jun 17, 2024)
2-174349010-A-T		not specified	Uncertain significance (Aug 02, 2021)
2-174349085-A-C		not specified	Uncertain significance (May 26, 2023)
2-174349153-T-C		not specified	Uncertain significance (Sep 20, 2024)
2-174350726-C-A		not specified	Uncertain significance (Dec 06, 2021)
2-174350729-T-A		not specified	Uncertain significance (Mar 22, 2023)
2-174350743-C-G		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CIR1	protein_coding	protein_coding	ENST00000342016	10	47694

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.31e-8	0.857	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	179	223	0.804	0.0000113	3007
Missense in Polyphen		27	28.834	0.93638		426
Synonymous	-0.909	88	77.8	1.13	0.00000408	738
Loss of Function	1.60	15	23.3	0.643	0.00000134	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000531	0.000530
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000989	0.0000924
European (Non-Finnish)	0.000279	0.000273
Middle Eastern	0.000109	0.000109
South Asian	0.0000987	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate splice site selection during alternative splicing of pre-mRNAs (By similarity). Regulates transcription and acts as corepressor for RBPJ. Recruits RBPJ to the Sin3-histone deacetylase complex (HDAC). Required for RBPJ-mediated repression of transcription. {ECO:0000250, ECO:0000269|PubMed:19409814, ECO:0000269|PubMed:9874765}.
• Pathway: Notch signaling pathway - Homo sapiens (human);Notch Signaling Pathway;Notch (Consensus)

Intolerance Scores

• loftool: 0.255
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.611
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.814

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cir1
• Phenotype: embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; vision/eye phenotype; homeostasis/metabolism phenotype; skeleton phenotype; renal/urinary system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; craniofacial phenotype

Gene ontology

• Biological process: mRNA processing;RNA splicing;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm;centrosome;nuclear speck;protein-containing complex
• Molecular function: DNA-binding transcription factor activity;transcription corepressor activity;protein binding;protein kinase binding;protein-containing complex binding