BTN2A1

Chr 6

butyrophilin subfamily 2 member A1

Also known as: BK14H9.1, BT2.1, BTF1, BTN2.1, DJ3E1.1

NCBI Gene: 11120ENSG00000112763UniProt: Q7KYR7

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]

107
ClinVar variants
4
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— BTN2A1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
4 Pathogenic / Likely Pathogenic· 89 VUS of 107 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.83LOEUF
pLI 0.000
Z-score -1.53
OE 1.37 (1.01–1.83)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.44Z-score
OE missense 1.07 (0.98–1.18)
321 obs / 299.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.1.37 (1.01–1.83)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.07 (0.98–1.18)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.15
0≤1.21.6
LoF obs/exp: 27 / 19.7Missense obs/exp: 321 / 299.7Syn Z: -1.27

ClinVar Variant Classifications

107 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4
VUS89
Likely Benign13
Benign1
4
Pathogenic
89
VUS
13
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
4
0
4
Likely Pathogenic
0
0
0
0
0
VUS
0
83
6
0
89
Likely Benign
0
13
0
0
13
Benign
0
0
0
1
1
Total096101107

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

BTN2A1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
BTN2A1 targeting reprograms M2-like macrophages and TAMs via SYK and MAPK signaling.
Kerneur C et al.·Cell Rep
2024
Large-Scale Plasma Proteomics to Profile Pathways and Prognosis of Chronic Pain.
Li ZY et al.·Adv Sci (Weinh)
2025
Gamma delta TCR anti-CD3 bispecific molecules (GABs) as novel immunotherapeutic compounds.
van Diest E et al.·J Immunother Cancer
2021
Potential of gamma/delta T cells for solid tumor immunotherapy.
Zhu D et al.·Front Immunol
2024Review
Unusual Partners: γδ-TCR-Based T Cell Therapy in Combination with Oncolytic Virus Treatment for Diffuse Midline Gliomas.
Vazaios K et al.·Int J Mol Sci
2025
Genome-wide Mendelian randomization mapping the influence of plasma proteome on major depressive disorder.
Li C et al.·J Affect Disord
2025
A Brief Molecular History of Vγ9Vδ2 TCR-Mediated Phosphoantigen Sensing.
Mohammed F et al.·Immunol Rev
2025Review
BTN2A1 and BTN3A1 as Novel Coeliac Disease Risk Loci: An In Silico Analysis.
Luu Hoang KN et al.·Int J Mol Sci
2025
The making of multivalent gamma delta TCR anti-CD3 bispecific T cell engagers.
van Diest E et al.·Front Immunol
2023
A glance over the fence: Using phylogeny and species comparison for a better understanding of antigen recognition by human γδ T-cells.
Herrmann T et al.·Immunol Rev
2020Review
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools