CIB3

calcium and integrin binding family member 3, the group of EF-hand domain containing

Basic information

Region (hg38): 19:16161368-16173525

Links

ENSG00000141977 ∙ NCBI:117286 ∙ OMIM:610645 ∙ HGNC:24580 ∙ Uniprot:Q96Q77 ∙ 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 CIB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CIB3 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in CIB3

This is a list of pathogenic ClinVar variants found in the CIB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-16161473-G-C		not specified	Uncertain significance (Jun 09, 2022)
19-16164737-G-A		not specified	Uncertain significance (Sep 29, 2022)
19-16164772-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-16164835-G-A		not specified	Uncertain significance (Mar 18, 2024)
19-16164850-C-T		not specified	Uncertain significance (Aug 15, 2023)
19-16164851-G-A		not specified	Uncertain significance (May 09, 2024)
19-16168143-T-C		not specified	Uncertain significance (Sep 14, 2023)
19-16168179-C-G		not specified	Uncertain significance (Aug 17, 2021)
19-16168271-C-T		not specified	Uncertain significance (Aug 22, 2023)
19-16168272-G-A		not specified	Uncertain significance (Dec 11, 2023)
19-16168278-G-A		not specified	Uncertain significance (Mar 17, 2023)
19-16169632-T-G		not specified	Uncertain significance (May 31, 2023)
19-16169638-C-T		not specified	Uncertain significance (May 30, 2024)
19-16169664-G-A		not specified	Uncertain significance (Mar 26, 2024)
19-16169694-T-G		not specified	Uncertain significance (Dec 27, 2023)
19-16169705-G-A			Likely benign (Feb 01, 2023)
19-16169709-T-C		not specified	Uncertain significance (Jan 17, 2024)
19-16169716-C-T		not specified	Uncertain significance (May 31, 2022)
19-16169731-G-A		not specified	Uncertain significance (Mar 30, 2024)
19-16169731-G-T		not specified	Uncertain significance (Oct 27, 2023)
19-16169733-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CIB3	protein_coding	protein_coding	ENST00000269878	6	12158

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.34e-9	0.0416	125594	1	152	125747	0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0393	116	117	0.990	0.00000713	1249
Missense in Polyphen		41	49.092	0.83516		514
Synonymous	1.59	35	49.2	0.711	0.00000328	340
Loss of Function	-0.641	12	9.83	1.22	4.18e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000878	0.000878
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.000931	0.000878
European (Non-Finnish)	0.000616	0.000615
Middle Eastern	0.000164	0.000163
South Asian	0.00135	0.00134
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.737
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.454
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.373

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cib3

Gene ontology

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