BTN2A1
protein-codingbutyrophilin subfamily 2 member A1, the group of V-set domain containing|C2-set domain containing|Butyrophilins
Gene summary
This gene encodes a member of the immunoglobulin superfamily. The gene is located in a cluster of butyrophilin-like genes in the juxta-telomeric region of the major histocompatibility complex on chromosome 6. A pseudogene of this gene has been identified in this cluster. The encoded protein is an integral plasma membrane protein involved in lipid, fatty-acid, and sterol metabolism. Alterations in this gene may be associated with several disease states including metabolic syndrome. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.7 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 BTN2A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_007049.5. 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 | 1 | ||||
| missense | 85 | 14 | 99 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 90 | 14 | 1 | 105 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_008980.1 | 7 | MANE Select | |
| Ensembl | ENSP00000312158.5 | 7 | MANE Select | |
| RefSeq | NP_001184162.1 | 6 | Standard | |
| RefSeq | NP_001184163.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Butyrophilin (BTN) family interactions
- Immune System
- Adaptive Immune System
Biological Process
- lipid metabolic process
- regulation of immune response
- T cell receptor signaling pathway
Molecular Function
- molecular_function
- signaling receptor binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000312541
- Coding exons
- 7
- Length
- 18700
- Individuals with no LoFs
- 125575
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 173
- Defined
- 125748
- p
- 0.000688
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.438 | 321 | 300 | 1.07 | 0.0000177 | 3424 |
| Missense (PolyPhen) | 95 | 80.649 | 1.178 | 1054 | ||
| Synonymous | -1.27 | 141 | 123 | 1.15 | 0.00000766 | 1068 |
| Loss of Function | -1.53 | 27 | 19.7 | 1.37 | 0.00000111 | 222 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00074 | 0.00074 | rare |
| Latino/Admixed American | 0.00047 | 0.00046 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0013 | 0.0013 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00082 | 0.00082 | rare |
| South Asian | 0.00052 | 0.00052 | rare |
| Other | 0.0020 | 0.0020 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0898
Intolerance Scores
- LoFtool
- 0.979
- RVIS EVS
- 0.87
- RVIS percentile EVS
- 88.87
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.242
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |