CABIN1

calcineurin binding protein 1, the group of HIRA histone chaperone complex subunits

Basic information

Region (hg38): 22:24011192-24178628

Links

ENSG00000099991 ∙ NCBI:23523 ∙ OMIM:604251 ∙ HGNC:24187 ∙ Uniprot:Q9Y6J0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurofibromatosis (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CABIN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CABIN1 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				25	6	31
missense			127	11	14	152
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				6		6
non coding				4	20	24
Total	0	0	127	40	40

Variants in CABIN1

This is a list of pathogenic ClinVar variants found in the CABIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-24036093-G-A		not specified	Uncertain significance (Dec 09, 2023)
22-24036130-T-G		not specified	Benign (May 04, 2022)
22-24038358-C-T		not specified	Uncertain significance (Apr 01, 2024)
22-24038402-C-T		not specified	Uncertain significance (Jun 01, 2024)
22-24038422-A-C		not specified	Uncertain significance (Apr 20, 2024)
22-24038457-G-A		not specified	Uncertain significance (Jul 02, 2024)
22-24041145-T-G		not specified	Uncertain significance (Aug 28, 2024)
22-24041150-C-T		CABIN1-related disorder	Likely benign (Mar 29, 2018)
22-24041256-A-G		not specified	Uncertain significance (Sep 26, 2022)
22-24041599-G-G			Benign (Nov 10, 2018)
22-24042896-G-A		CABIN1-related disorder	Likely benign (Feb 21, 2019)
22-24042988-C-T		not specified	Uncertain significance (May 26, 2023)
22-24042989-G-A		not specified	Uncertain significance (Jul 05, 2022)
22-24043013-G-A		not specified	Uncertain significance (Jan 16, 2024)
22-24043022-C-A		not specified	Uncertain significance (Sep 14, 2022)
22-24043042-G-A		not specified	Uncertain significance (Apr 04, 2024)
22-24049157-A-G		not specified	Uncertain significance (May 28, 2024)
22-24049186-C-T		not specified	Uncertain significance (Feb 21, 2024)
22-24049199-C-T		not specified	Uncertain significance (Mar 24, 2023)
22-24050833-C-T		not specified	Uncertain significance (Jan 23, 2023)
22-24050839-A-G		not specified	Uncertain significance (Nov 21, 2024)
22-24050841-G-A		CABIN1-related disorder	Benign (May 04, 2021)
22-24050883-G-A		not specified	Uncertain significance (Jul 25, 2024)
22-24050908-G-A		not specified	Uncertain significance (May 26, 2023)
22-24050917-T-C		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CABIN1	protein_coding	protein_coding	ENST00000398319	36	166955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.28e-17	1.00	125625	0	123	125748	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	1059	1.25e+3	0.847	0.0000801	14388
Missense in Polyphen		420	556.26	0.75504		6700
Synonymous	-0.207	533	527	1.01	0.0000344	4537
Loss of Function	4.99	45	98.5	0.457	0.00000525	1178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000858	0.000857
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000381	0.000381
Finnish	0.000194	0.000185
European (Non-Finnish)	0.000609	0.000580
Middle Eastern	0.000381	0.000381
South Asian	0.000591	0.000588
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be required for replication-independent chromatin assembly. May serve as a negative regulator of T-cell receptor (TCR) signaling via inhibition of calcineurin. Inhibition of activated calcineurin is dependent on both PKC and calcium signals. Acts as a negative regulator of p53/TP53 by keeping p53 in an inactive state on chromatin at promoters of a subset of it's target genes. {ECO:0000269|PubMed:14718166, ECO:0000269|PubMed:9655484}.
• Pathway: role of mef2d in t-cell apoptosis;Formation of Senescence-Associated Heterochromatin Foci (SAHF);DNA Damage/Telomere Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;TCR;Cellular responses to external stimuli;control of skeletal myogenesis by hdac and calcium/calmodulin-dependent kinase (camk);Role of Calcineurin-dependent NFAT signaling in lymphocytes;Calcium signaling in the CD4+ TCR pathway (Consensus)

Intolerance Scores

• loftool: 0.723
• rvis_EVS: -0.66
• rvis_percentile_EVS: 15.95

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.706
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.800

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cabin1
• Phenotype: immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: DNA replication-independent nucleosome assembly;cell surface receptor signaling pathway;negative regulation of phosphoprotein phosphatase activity
• Cellular component: nucleus;nucleoplasm;cytosol;aggresome
• Molecular function: protein phosphatase inhibitor activity;nucleosome binding