BTNL9

protein-coding

butyrophilin like 9, the group of V-set domain containing|Butyrophilins

Gene summary

Predicted to enable signaling receptor binding activity. Predicted to be involved in T cell receptor signaling pathway and regulation of cytokine production. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152547.5

Inheritance

—

ClinVar variants

U:117B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr5:181,040,225-181,061,521

External References & Databases

Ensembl (ENSG00000165810)

Transcript & Mutation Effects

hg38 • Region Span ~21.3 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 BTNL9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152547.5. 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			3 clinvar	1 clinvar	4 clinvar	8
missense			108 clinvar	4 clinvar		112
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	117	5	5	127

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152547.5	RefSeq	NP_689760.2	10	MANE Select
ENST00000327705.14	Ensembl	ENSP00000330200.9	10	MANE Select
NM_001308245.2	RefSeq	NP_001295174.1	9	Standard
ENST00000376841.6	Ensembl	ENSP00000366037.2	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

regulation of immune response
T cell receptor signaling pathway

Molecular Function

signaling receptor 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: ENST00000327705
Coding exons: 10
Length: 21299
Individuals with no LoFs: 123855
Homozygous LoFs: 9
Heterozygous LoFs: 1884
Defined: 125748
p: 0.00756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.554	319	292	1.09	0.0000151	3380
Missense (PolyPhen)		117	98.985	1.182		1216
Synonymous	-0.556	145	137	1.06	0.00000753	1104
Loss of Function	0.277	21	22.4	0.937	0.00000105	245

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0025	0.0025	notable
Latino/Admixed American	0.0087	0.0087	notable
Ashkenazi Jewish	0.0013	0.0013	notable
East Asian	0.0026	0.0026	notable
Finnish	0.00074	0.00074	rare
European (Non-Finnish)	0.010	0.010	notable
South Asian	0.0094	0.0093	notable
Other	0.0078	0.0078	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.882
RVIS EVS: -0.13
RVIS percentile EVS: 43.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0803

Gene Damage Prediction

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