CIB4

calcium and integrin binding family member 4, the group of EF-hand domain containing

Basic information

Region (hg38): 2:26581205-26641366

Links

ENSG00000157884 ∙ NCBI:130106 ∙ OMIM:610646 ∙ HGNC:33703 ∙ Uniprot:A0PJX0 ∙ 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 CIB4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CIB4 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in CIB4

This is a list of pathogenic ClinVar variants found in the CIB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-26581385-C-T		not specified	Uncertain significance (Jan 27, 2022)
2-26582855-T-C		not specified	Uncertain significance (Sep 17, 2021)
2-26582861-A-G		not specified	Uncertain significance (Jun 23, 2021)
2-26582889-T-C		not specified	Uncertain significance (Nov 09, 2023)
2-26582900-G-A		not specified	Uncertain significance (May 18, 2023)
2-26583796-G-T		not specified	Uncertain significance (Dec 23, 2024)
2-26583844-C-T		not specified	Uncertain significance (Oct 20, 2023)
2-26583866-C-T		not specified	Uncertain significance (Jan 03, 2022)
2-26583895-A-C		not specified	Uncertain significance (Jun 07, 2024)
2-26595185-G-A		not specified	Uncertain significance (Dec 03, 2024)
2-26595299-G-A		not specified	Uncertain significance (Jun 16, 2024)
2-26629411-C-T		not specified	Uncertain significance (Oct 06, 2022)
2-26629436-G-T		not specified	Uncertain significance (Apr 20, 2024)
2-26629495-G-T		not specified	Uncertain significance (Nov 02, 2023)
2-26640549-T-C		not specified	Uncertain significance (Dec 14, 2022)
2-26640556-G-T		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CIB4	protein_coding	protein_coding	ENST00000288861	7	60167

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.11e-7	0.196	125662	1	85	125748	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.237	110	103	1.07	0.00000534	1241
Missense in Polyphen		36	30.668	1.1739		383
Synonymous	0.294	36	38.3	0.940	0.00000198	315
Loss of Function	0.166	11	11.6	0.948	6.49e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000417	0.000417
Ashkenazi Jewish	0.00	0.00
East Asian	0.00163	0.00163
Finnish	0.00	0.00
European (Non-Finnish)	0.000317	0.000316
Middle Eastern	0.00163	0.00163
South Asian	0.000327	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.830
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.0787
• hipred: N
• hipred_score: 0.199

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.100

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cib4

Gene ontology

• Molecular function: magnesium ion binding;calcium ion binding;protein binding