EFCAB3
protein-codingEF-hand calcium binding domain 3, 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
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~72.5 kbGenCC 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 EFCAB3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_173503.4. 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 | 1 | ||||
| missense | 38 | 2 | 1 | 41 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 38 | 4 | 2 | 44 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_775774.1 | 9 | MANE Select | |
| Ensembl | ENSP00000302649.3 | 9 | MANE Select | |
| RefSeq | NP_001138405.1 | 12 | Standard | |
| Ensembl | ENSP00000403932.2 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Pathways in clear cell renal cell carcinoma
Molecular Function
- calcium ion binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000450662
- Coding exons
- 12
- Length
- 46259
- Individuals with no LoFs
- 123449
- Homozygous LoFs
- 29
- Heterozygous LoFs
- 2268
- Defined
- 125746
- p
- 0.00918
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.759 | 211 | 244 | 0.863 | 0.0000111 | 3250 |
| Missense (PolyPhen) | 68 | 72.784 | 0.93427 | 1058 | ||
| Synonymous | -0.621 | 92 | 84.7 | 1.09 | 0.00000383 | 863 |
| Loss of Function | 1.50 | 17 | 25.1 | 0.677 | 0.00000140 | 321 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.019 | 0.019 | notable |
| Latino/Admixed American | 0.0027 | 0.0026 | notable |
| Ashkenazi Jewish | 0.0018 | 0.0018 | notable |
| East Asian | 0.00066 | 0.00065 | rare |
| Finnish | 0.046 | 0.045 | notable |
| European (Non-Finnish) | 0.0075 | 0.0074 | notable |
| South Asian | 0.0014 | 0.0013 | notable |
| Other | 0.0058 | 0.0057 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.760
- RVIS EVS
- 0.66
- RVIS percentile EVS
- 84.55
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |