EFCAB13

protein-coding

EF-hand calcium binding domain 13, the group of EF-hand domain containing

Gene summary

Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C17orf57

MANE transcript

NM_152347.5

Inheritance

—

ClinVar variants

U:117B:28

Top phenotype

EFCAB13-related disorder

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chr17:47,323,290-47,441,312

External References & Databases

Ensembl (ENSG00000178852)

Transcript & Mutation Effects

hg38 • Region Span ~118.0 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 EFCAB13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 114

EFCAB13-related disorderTotal: 19

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152347.5. 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			2 clinvar	4 clinvar	6 clinvar	12
missense			106 clinvar	10 clinvar	3 clinvar	119
nonsense			1 clinvar	1 clinvar	1 clinvar	3
start loss						0
frameshift				1 clinvar	1 clinvar	2
splice donor/acceptor (+/-2bp)			8 clinvar		1 clinvar	9
Total	0	0	117	16	12	145

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152347.5	RefSeq	NP_689560.3	22	MANE Select
ENST00000331493.7	Ensembl	ENSP00000332111.2	22	MANE Select
NM_001195192.2	RefSeq	NP_001182121.1	19	Standard
NM_001426585.1	RefSeq	NP_001413514.1	21	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000331493
Coding exons: 22
Length: 118023
Individuals with no LoFs: 30848
Homozygous LoFs: 30813
Heterozygous LoFs: 64078
Defined: 125739
p: 0.505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.00	412	473	0.870	0.0000225	6497
Missense (PolyPhen)		88	94.504	0.93118		1542
Synonymous	1.67	135	162	0.833	0.00000792	1660
Loss of Function	-0.417	46	43.0	1.07	0.00000196	645

Population LoF Frequency

Population	CAF	p-value	Status
African	0.65	0.56	notable
Latino/Admixed American	0.40	0.38	notable
Ashkenazi Jewish	0.57	0.56	notable
East Asian	0.42	0.42	notable
Finnish	0.53	0.52	notable
European (Non-Finnish)	0.56	0.56	notable
South Asian	0.48	0.47	notable
Other	0.54	0.53	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.89
RVIS percentile EVS: 89.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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