NECAB1

protein-coding

N-terminal EF-hand calcium binding protein 1, the group of EF-hand domain containing|N-terminal EF-hand calcium binding proteins

Gene summary

Enables identical protein binding activity. Predicted to be involved in regulation of amyloid precursor protein biosynthetic process. Predicted to act upstream of or within blastocyst hatching. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

EFCBP1

MANE transcript

NM_022351.5

Inheritance

—

ClinVar variants

U:43B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr8:90,791,741-90,959,393

External References & Databases

Ensembl (ENSG00000123119)

Transcript & Mutation Effects

hg38 • Region Span ~167.7 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 NECAB1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 41

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022351.5. 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				1 clinvar		1
missense			41 clinvar	2 clinvar		43
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	43	3	0	46

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022351.5	RefSeq	NP_071746.1	13	MANE Select
ENST00000417640.7	Ensembl	ENSP00000387380.2	13	MANE Select
ENST00000521366.1	Ensembl	ENSP00000428632.1	4	Standard
ENST00000521366.2	Ensembl	ENSP00000428632.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

blastocyst hatching
biological_process
regulation of amyloid precursor protein biosynthetic process

Molecular Function

molecular_function
calcium ion binding

Cellular Component

cellular_component
nucleus
nucleoplasm
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000417640
Coding exons: 13
Length: 167859
Individuals with no LoFs: 124615
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 124627
p: 0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.14	128	170	0.754	0.00000862	2313
Missense (PolyPhen)		27	49.716	0.54308		686
Synonymous	1.11	50	61.0	0.820	0.00000310	588
Loss of Function	3.04	7	22.6	0.309	0.00000115	284

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.000037	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.500
RVIS EVS: -0.07
RVIS percentile EVS: 48.12

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.193

Gene Damage Prediction

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