BTNL3

protein-coding

butyrophilin like 3, the group of V-set domain containing|Butyrophilins

Gene summary

Predicted to enable signaling receptor binding activity. Involved in extrathymic T cell selection. Predicted to be located in membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_197975.3

Inheritance

—

ClinVar variants

U:63B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr5:180,988,846-181,006,727

External References & Databases

Ensembl (ENSG00000168903)

Transcript & Mutation Effects

hg38 • Region Span ~17.9 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 BTNL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 69

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_197975.3. 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
missense			63 clinvar	7 clinvar	2 clinvar	72
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	8	3	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_197975.3	RefSeq	NP_932079.1	8	MANE Select
ENST00000342868.7	Ensembl	ENSP00000341787.6	8	MANE Select
ENST00000899564.1	Ensembl	ENSP00000569623.1	8	Standard
ENST00000899564.2	Ensembl	ENSP00000569623.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
regulation of immune response
T cell receptor signaling pathway

Molecular Function

molecular_function
signaling receptor binding

Cellular Component

cellular_component
external side of plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000342868
Coding exons: 8
Length: 17883
Individuals with no LoFs: 125147
Homozygous LoFs: 3
Heterozygous LoFs: 13
Defined: 125163
p: 0.0000639

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.677	229	260	0.882	0.0000140	3011
Missense (PolyPhen)		56	68.608	0.81624		915
Synonymous	0.867	92	103	0.891	0.00000599	911
Loss of Function	2.03	8	17.0	0.470	7.88e-7	193

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00035	0.00026	rare
Latino/Admixed American	0.000097	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00023	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000051	0.000026	rare
South Asian	0.000068	0.000065	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0614

Intolerance Scores

LoFtool: 0.784
RVIS EVS: 1.29
RVIS percentile EVS: 93.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.165

Gene Damage Prediction

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