EFHB

protein-coding

EF-hand domain family member B, the group of EF-hand domain containing|Cilia and flagella associated

Gene summary

Enables calcium ion sensor activity. Involved in regulation of calcineurin-NFAT signaling cascade and regulation of store-operated calcium entry. Located in axonemal microtubule. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_144715.4

Inheritance

—

ClinVar variants

P:1U:122B:8

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr3:19,879,472-19,947,025

External References & Databases

Ensembl (ENSG00000163576)

Transcript & Mutation Effects

hg38 • Region Span ~67.6 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 EFHB variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 123

not providedTotal: 4

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144715.4. 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 clinvar		2
missense			120 clinvar	7 clinvar		127
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	122	8	0	131

Highest pathogenic variant AF is 0.0008165885

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144715.4	RefSeq	NP_653316.3	13	MANE Select
ENST00000295824.14	Ensembl	ENSP00000295824.9	13	MANE Select
NM_001330688.2	RefSeq	NP_001317617.1	14	Standard
ENST00000344838.8	Ensembl	ENSP00000342263.4	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

calcium ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295824
Coding exons: 13
Length: 67554
Individuals with no LoFs: 124327
Homozygous LoFs: 21
Heterozygous LoFs: 1245
Defined: 125593
p: 0.00505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.242	448	434	1.03	0.0000222	5426
Missense (PolyPhen)		66	60.114	1.0979		751
Synonymous	1.20	130	149	0.875	0.00000732	1581
Loss of Function	0.333	37	39.3	0.943	0.00000240	496

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.0011	notable
Latino/Admixed American	0.026	0.026	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0092	0.0090	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.0014	0.0014	notable
South Asian	0.00073	0.00069	rare
Other	0.0043	0.0043	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.983
RVIS EVS: 1.96
RVIS percentile EVS: 97.55

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0834

Gene Damage Prediction

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