BTN3A1

protein-coding

butyrophilin subfamily 3 member A1, the group of V-set domain containing|CD molecules|C2-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., BNT3A1) 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

NM_007048.6

Inheritance

—

ClinVar variants

U:66B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr6:26,402,237-26,415,208

External References & Databases

Ensembl (ENSG00000026950)

Transcript & Mutation Effects

hg38 • Region Span ~13.0 kb

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GenCC 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 BTN3A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007048.6. 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 clinvar	1
missense			59 clinvar	6 clinvar		65
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	66	7	1	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007048.6	RefSeq	NP_008979.3	9	MANE Select
ENST00000289361.11	Ensembl	ENSP00000289361.6	9	MANE Select
NM_001145008.2	RefSeq	NP_001138480.1	9	Standard
NM_001145009.2	RefSeq	NP_001138481.1	9	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

adaptive immune response
cytokine secretion
regulation of immune response
activated T cell proliferation
T cell receptor signaling pathway

Molecular Function

signaling receptor binding
protein binding

Cellular Component

plasma membrane
external side of plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000289361
Coding exons: 9
Length: 12980
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.185	261	270	0.968	0.0000141	3338
Missense (PolyPhen)		64	88.981	0.71925		1232
Synonymous	2.28	76	106	0.718	0.00000615	996
Loss of Function	0.917	15	19.4	0.775	0.00000105	215

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00023	0.00023	rare
Other	0.00020	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in T-cell activation and in the adaptive immune response. Regulates the proliferation of activated T-cells. Regulates the release of cytokines and IFNG by activated T-cells. Mediates the response of T-cells toward infected and transformed cells that are characterized by high levels of phosphorylated metabolites, such as isopentenyl pyrophosphate. {ECO:0000269|PubMed:21113407, ECO:0000269|PubMed:21918970, ECO:0000269|PubMed:22767497, ECO:0000269|PubMed:22846996}.;

Recessive Scores

pRec: 0.0771

Intolerance Scores

LoFtool: 0.987
RVIS EVS: 0.53
RVIS percentile EVS: 80.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.115

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium