BTN3A1

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

Basic information

Region (hg38): 6:26402236-26415208

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.

• Inborn genetic diseases (18 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			16	3		19
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	4	1

Variants in BTN3A1

This is a list of pathogenic ClinVar variants found in the BTN3A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-26405913-G-C		not specified	Uncertain significance (Dec 13, 2022)
6-26406092-G-A		not specified	Uncertain significance (Oct 20, 2021)
6-26406094-G-A		not specified	Uncertain significance (Jun 07, 2023)
6-26406206-T-C		not specified	Uncertain significance (Mar 24, 2023)
6-26407799-C-A		not specified	Uncertain significance (Jun 29, 2023)
6-26407815-C-G		not specified	Uncertain significance (Feb 14, 2023)
6-26407828-C-A		not specified	Uncertain significance (Nov 03, 2023)
6-26407917-T-A			Likely benign (Jan 31, 2018)
6-26409554-A-G		not specified	Uncertain significance (Jun 22, 2021)
6-26409568-G-T		not specified	Uncertain significance (Jul 31, 2023)
6-26409605-T-C		not specified	Uncertain significance (Dec 15, 2022)
6-26409631-C-A		not specified	Uncertain significance (Oct 26, 2021)
6-26409653-C-G		not specified	Uncertain significance (May 31, 2022)
6-26409697-G-T		not specified	Uncertain significance (Nov 06, 2023)
6-26413274-C-T		not specified	Uncertain significance (Jan 10, 2023)
6-26413296-T-A			Likely benign (Jul 02, 2018)
6-26413345-G-A		not specified	Uncertain significance (Dec 28, 2022)
6-26413363-A-G		not specified	Uncertain significance (Jul 13, 2021)
6-26413403-G-A		not specified	Likely benign (Jan 09, 2023)
6-26413477-A-G		not specified	Likely benign (May 26, 2022)
6-26413486-G-A		not specified	Uncertain significance (Jan 23, 2024)
6-26413492-A-G		not specified	Uncertain significance (Jan 23, 2023)
6-26413595-T-C		not specified	Uncertain significance (Apr 18, 2023)
6-26413612-G-A		not specified	Uncertain significance (Jan 26, 2023)
6-26413615-T-C		not specified	Uncertain significance (Jan 03, 2024)

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