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.

not_specified (278 variants)
not_provided (46 variants)
CABIN1-related_disorder (46 variants)
Prostate_cancer (1 variants)

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. These statistics are base on transcript: NM_000012295.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				24 clinvar	6 clinvar	30
missense			271 clinvar	12 clinvar	10 clinvar	293
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	271	36	16

Loading clinvar variants...

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

pHI
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