EFCAB7
protein-codingEF-hand calcium binding domain 7, the group of EF-hand domain containing
Gene summary
Predicted to enable calcium ion binding activity. Predicted to be involved in positive regulation of protein import into nucleus; positive regulation of protein localization to ciliary membrane; and positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasmic side of plasma membrane. Predicted to be part of plasma membrane protein complex. Predicted to be active in ciliary membrane. [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 ~49.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0021003
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EFCAB7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032437.4. 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 | 66 | 2 | 2 | 70 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 71 | 3 | 2 | 76 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115813.2 | 13 | MANE Select | |
| Ensembl | ENSP00000360129.4 | 13 | MANE Select | |
| Ensembl | ENSP00000597196.1 | 13 | Standard | |
| Ensembl | ENSP00000641396.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Signal Transduction
- Activation of SMO
- Hedgehog ,on, state
- Signaling by Hedgehog
Biological Process
- positive regulation of protein import into nucleus
- positive regulation of transcription by RNA polymerase II
- positive regulation of protein localization to ciliary membrane
Molecular Function
- calcium ion binding
Cellular Component
- cilium
- extrinsic component of membrane
- ciliary membrane
- plasma membrane protein complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371088
- Coding exons
- 13
- Length
- 49322
- Individuals with no LoFs
- 125568
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 172
- Defined
- 125740
- p
- 0.000684
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 255 | 306 | 0.834 | 0.0000142 | 4155 |
| Missense (PolyPhen) | 42 | 59.005 | 0.71181 | 856 | ||
| Synonymous | 1.04 | 93 | 107 | 0.872 | 0.00000531 | 1117 |
| Loss of Function | 0.687 | 28 | 32.2 | 0.869 | 0.00000183 | 420 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00077 | 0.00068 | rare |
| Latino/Admixed American | 0.0011 | 0.00067 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0010 | 0.00082 | notable |
| Finnish | 0.00047 | 0.00037 | rare |
| European (Non-Finnish) | 0.00097 | 0.00084 | rare |
| South Asian | 0.00062 | 0.00049 | rare |
| Other | 0.00083 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the EvC complex that positively regulates ciliary Hedgehog (Hh) signaling. Required for the localization of the EVC2:EVC subcomplex at the base of primary cilia. {ECO:0000250|UniProtKB:Q8VDY4}.;
Intolerance Scores
- LoFtool
- 0.951
- RVIS EVS
- 1.62
- RVIS percentile EVS
- 96.03
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.151
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |