EFCAB5

protein-coding

EF-hand calcium binding domain 5, the group of EF-hand domain containing

Gene summary

Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_198529.4

Inheritance

—

ClinVar variants

U:179B:44

Top phenotype

EFCAB5-related disorder

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr17:29,929,200-30,108,452

External References & Databases

Ensembl (ENSG00000176927)

Transcript & Mutation Effects

hg38 • Region Span ~179.3 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 EFCAB5 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 195

EFCAB5-related disorderTotal: 24

not providedTotal: 8

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198529.4. 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				9 clinvar	2 clinvar	11
missense			177 clinvar	25 clinvar	6 clinvar	208
nonsense				1 clinvar		1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar	1 clinvar		2
Total	0	0	179	36	8	223

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198529.4	RefSeq	NP_940931.3	23	MANE Select
ENST00000394835.8	Ensembl	ENSP00000378312.3	23	MANE Select
NM_001145053.2	RefSeq	NP_001138525.2	13	Standard
ENST00000419434.5	Ensembl	ENSP00000417009.1	18	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: ENST00000394835
Coding exons: 23
Length: 179253
Individuals with no LoFs: 122492
Homozygous LoFs: 15
Heterozygous LoFs: 2132
Defined: 124639
p: 0.00865

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.890	672	740	0.908	0.0000360	9888
Missense (PolyPhen)		213	237.46	0.89699		3250
Synonymous	0.482	255	265	0.962	0.0000133	2693
Loss of Function	2.66	47	71.2	0.660	0.00000348	952

Population LoF Frequency

Population	CAF	p-value	Status
African	0.012	0.012	notable
Latino/Admixed American	0.0026	0.0025	notable
Ashkenazi Jewish	0.0058	0.0055	notable
East Asian	0.020	0.020	notable
Finnish	0.020	0.020	notable
European (Non-Finnish)	0.0092	0.0085	notable
South Asian	0.0018	0.0017	notable
Other	0.0072	0.0070	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.997
RVIS EVS: 2.23
RVIS percentile EVS: 98.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0235

Gene Damage Prediction

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