CIB3

protein-coding

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

Gene summary

This gene product shares a high degree of sequence similarity with DNA-dependent protein kinase catalytic subunit-interacting protein 2 in human and mouse, and like them may bind the catalytic subunit of DNA-dependent protein kinases. The exact function of this gene is not known. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

MANE transcript

NM_054113.4

Inheritance

—

ClinVar variants

U:38B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.22

Max pathogenic AF

—

Genomic locus

chr19:16,161,368-16,173,525

External References & Databases

Ensembl (ENSG00000141977)

Transcript & Mutation Effects

hg38 • Region Span ~12.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CIB3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_054113.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			38 clinvar	1 clinvar		39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	2	0	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_054113.4	RefSeq	NP_473454.1	6	MANE Select
ENST00000269878.8	Ensembl	ENSP00000269878.3	6	MANE Select
NM_001300922.2	RefSeq	NP_001287851.1	4	Standard
ENST00000379859.7	Ensembl	ENSP00000369188.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

magnesium ion binding
calcium ion binding
protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269878
Coding exons: 6
Length: 12158
Individuals with no LoFs: 125594
Homozygous LoFs: 1
Heterozygous LoFs: 152
Defined: 125747
p: 0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0393	116	117	0.990	0.00000713	1249
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00093	0.00088	rare
European (Non-Finnish)	0.00062	0.00062	rare
South Asian	0.0014	0.0013	notable
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.737
RVIS EVS: -0.16
RVIS percentile EVS: 41.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.373

Gene Damage Prediction

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