BTN1A1

protein-coding

butyrophilin subfamily 1 member A1, the group of V-set domain containing|C2-set domain containing|Butyrophilins

Gene summary

Butyrophilin is the major protein associated with fat droplets in the milk. It is a member of the immunoglobulin superfamily. It may have a cell surface receptor function. The human butyrophilin gene is localized in the major histocompatibility complex (MHC) class I region of 6p and may have arisen relatively recently in evolution by the shuffling of exons between 2 ancestral gene families [provided by RefSeq, Jul 2008]

Previous symbols:

MANE transcript

NM_001732.3

Inheritance

—

ClinVar variants

U:69B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr6:26,500,303-26,510,425

External References & Databases

Ensembl (ENSG00000124557)

Transcript & Mutation Effects

hg38 • Region Span ~10.1 kb

Loading mutation effect viewer...

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 BTN1A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 69

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001732.3. 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 clinvar	2
missense			67 clinvar	3 clinvar	2 clinvar	72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	69	3	3	75

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001732.3	RefSeq	NP_001723.2	7	MANE Select
ENST00000684113.1	Ensembl	ENSP00000507193.1	7	MANE Select
ENST00000244513.10	Ensembl	ENSP00000244513.6	7	Standard
ENST00000244513.11	Ensembl	ENSP00000244513.6	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

regulation of immune response
T cell receptor signaling pathway

Molecular Function

signaling receptor binding
signaling receptor activity

Cellular Component

extracellular space
plasma membrane
integral component of plasma membrane
external side of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000244513
Coding exons: 7
Length: 9202
Individuals with no LoFs: 125670
Homozygous LoFs: 0
Heterozygous LoFs: 78
Defined: 125748
p: 0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.32	229	293	0.783	0.0000144	3383
Missense (PolyPhen)		64	101.67	0.62946		1216
Synonymous	1.67	95	118	0.805	0.00000577	1090
Loss of Function	1.26	15	21.3	0.704	9.81e-7	252

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0015	notable
Latino/Admixed American	0.00044	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.00033	0.00033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function in the secretion of milk-fat droplets. May act as a specific membrane-associated receptor for the association of cytoplasmic droplets with the apical plasma membrane (By similarity). Inhibits the proliferation of CD4 and CD8 T-cells activated by anti-CD3 antibodies, T-cell metabolism and IL2 and IFNG secretion (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.200

Intolerance Scores

LoFtool: 0.882
RVIS EVS: 0.84
RVIS percentile EVS: 88.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00414

Gene Damage Prediction

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