BCAS3
protein-codingBCAS3 microtubule associated cell migration factor, the group of WD repeat domain containing
Gene summary
Enables several functions, including acetyltransferase activator activity; beta-tubulin binding activity; and histone acetyltransferase binding activity. Involved in cellular response to estrogen stimulus; positive regulation of catalytic activity; and positive regulation of transcription by RNA polymerase II. Located in euchromatin; nucleus; and phagophore assembly site. Implicated in Hengel-Maroofian-Schols syndrome. Biomarker of breast cancer. [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 ~715.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0859208
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0859208
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0859208
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BCAS3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017679.5. 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 | 6 | 1 | 9 | ||
| missense | 3 | 118 | 3 | 1 | 125 | |
| nonsense | 1 | 8 | 1 | 10 | ||
| start loss | 0 | |||||
| frameshift | 3 | 3 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 8 | 11 | |||
| Total | 1 | 17 | 129 | 9 | 2 | 158 |
Highest pathogenic variant AF is 0.000024247489
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060149.3 | 23 | MANE Select | |
| Ensembl | ENSP00000385323.2 | 23 | MANE Select | |
| RefSeq | NP_001092902.1 | 24 | Standard | |
| RefSeq | NP_001307399.1 | 25 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ectoderm Differentiation
Biological Process
- angiogenesis
- Golgi organization
- positive regulation of endothelial cell migration
- microtubule organizing center organization
- negative regulation of GTPase activity
Molecular Function
- chromatin binding
- protein binding
- transcription factor binding
- acetyltransferase activator activity
- histone acetyltransferase binding
Cellular Component
- nucleus
- nucleolus
- cytoplasm
- cytoplasmic microtubule
- cell leading edge
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000390652
- Coding exons
- 24
- Length
- 715386
- Individuals with no LoFs
- 124771
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 37
- Defined
- 124808
- p
- 0.000148
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.60 | 375 | 546 | 0.687 | 0.0000307 | 6050 |
| Missense (PolyPhen) | 153 | 224.41 | 0.68178 | 2416 | ||
| Synonymous | 0.226 | 192 | 196 | 0.979 | 0.0000114 | 1840 |
| Loss of Function | 4.80 | 18 | 57.2 | 0.315 | 0.00000358 | 574 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.00032 | 0.00032 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00017 | 0.00017 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.000099 | 0.000098 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving BCAS3 has been found in some breast carcinoma cell lines. Translocation t(17;20)(q23;q13) with BCAS4.;
Intolerance Scores
- LoFtool
- 0.479
- RVIS EVS
- -0.75
- RVIS percentile EVS
- 13.67
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.948
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |