BTN3A3
protein-codingbutyrophilin subfamily 3 member A3, the group of V-set domain containing|Butyrophilins
Gene summary
The butyrophilin (BTN) genes are a group of major histocompatibility complex (MHC)-associated genes that encode type I membrane proteins with 2 extracellular immunoglobulin (Ig) domains and an intracellular B30.2 (PRYSPRY) domain. Three subfamilies of human BTN genes are located in the MHC class I region: the single-copy BTN1A1 gene (MIM 601610) and the BTN2 (e.g., BTN2A1; MIM 613590) and BTN3 (e.g., BNT3A3) genes, which have undergone tandem duplication, resulting in 3 copies of each (summary by Smith et al., 2010 [PubMed 20208008]).[supplied by OMIM, Nov 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.9 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 BTN3A3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006994.5. 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 | 2 | 3 | |||
| missense | 100 | 10 | 110 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 106 | 13 | 0 | 119 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_008925.1 | 9 | MANE Select | |
| Ensembl | ENSP00000244519.2 | 9 | MANE Select | |
| RefSeq | NP_001229732.1 | 5 | Standard | |
| RefSeq | NP_932078.2 | 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
- T cell mediated immunity
- regulation of immune response
- T cell receptor signaling pathway
Molecular Function
- signaling receptor binding
Cellular Component
- plasma membrane
- external side of plasma membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000244519
- Coding exons
- 9
- Length
- 12944
- Individuals with no LoFs
- 123785
- Homozygous LoFs
- 33
- Heterozygous LoFs
- 1929
- Defined
- 125747
- p
- 0.00783
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.152 | 335 | 327 | 1.02 | 0.0000179 | 3789 |
| Missense (PolyPhen) | 91 | 84.579 | 1.0759 | 1074 | ||
| Synonymous | -1.00 | 145 | 130 | 1.11 | 0.00000798 | 1183 |
| Loss of Function | -0.850 | 25 | 20.8 | 1.20 | 0.00000122 | 213 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0024 | 0.0023 | notable |
| Latino/Admixed American | 0.0051 | 0.0052 | notable |
| Ashkenazi Jewish | 0.045 | 0.044 | notable |
| East Asian | 0.0023 | 0.0022 | notable |
| Finnish | 0.0045 | 0.0044 | notable |
| European (Non-Finnish) | 0.0075 | 0.0074 | notable |
| South Asian | 0.0086 | 0.0085 | notable |
| Other | 0.012 | 0.012 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in T-cell responses in the adaptive immune response. {ECO:0000269|PubMed:22767497}.;
Recessive Scores
- pRec
- 0.0958
Intolerance Scores
- LoFtool
- 0.988
- RVIS EVS
- -0.28
- RVIS percentile EVS
- 33.49
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.447
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |