BTN3A1

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

Basic information

Region (hg38): 6:26402237-26415208

Links

ENSG00000026950 ∙ NCBI:11119 ∙ OMIM:613593 ∙ HGNC:1138 ∙ Uniprot:O00481 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BTN3A1 gene.

• not_specified (55 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTN3A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007048.6. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			51	5		56
nonsense				1		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	6	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTN3A1	protein_coding	protein_coding	ENST00000289361	9	12980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.87e-9	0.417	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.185	261	270	0.968	0.0000141	3338
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000331
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.000113	0.000109
South Asian	0.000232	0.000229
Other	0.000201	0.000163

dbNSFP

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}.
• Pathway: Butyrophilin (BTN) family interactions;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0771

Intolerance Scores

• loftool: 0.987
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.88

Haploinsufficiency Scores

• pHI: 0.0679
• hipred: N
• hipred_score: 0.112
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.115

Gene Damage Prediction

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

Gene ontology

• Biological process: adaptive immune response;cytokine secretion;regulation of immune response;activated T cell proliferation;T cell receptor signaling pathway;interferon-gamma secretion
• Cellular component: plasma membrane;external side of plasma membrane;integral component of membrane
• Molecular function: signaling receptor binding;protein binding