BTN2A2

butyrophilin subfamily 2 member A2, the group of V-set domain containing|C2-set domain containing|Butyrophilins

Basic information

Region (hg38): 6:26383096-26394874

Links

ENSG00000124508 ∙ NCBI:10385 ∙ OMIM:613591 ∙ HGNC:1137 ∙ Uniprot:Q8WVV5 ∙ 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 BTN2A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTN2A2 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				5	2	7
missense			33	6	9	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding					1	1
Total	0	0	33	11	12

Variants in BTN2A2

This is a list of pathogenic ClinVar variants found in the BTN2A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-26383832-C-T			Benign (Jan 03, 2019)
6-26383834-G-A		not specified	Uncertain significance (Feb 27, 2023)
6-26383864-C-T		not specified	Uncertain significance (Mar 20, 2023)
6-26383868-T-C		not specified	Uncertain significance (Oct 18, 2021)
6-26383878-G-A		BTN2A2-related disorder	Benign (Apr 29, 2019)
6-26383900-T-C		not specified	Uncertain significance (Sep 30, 2024)
6-26385032-G-T		not specified	Uncertain significance (Oct 03, 2023)
6-26385035-C-A		not specified	Uncertain significance (Oct 17, 2023)
6-26385035-C-G			Benign (Jan 03, 2019)
6-26385063-G-T		not specified	Uncertain significance (May 27, 2022)
6-26385098-G-A		not specified	Uncertain significance (Jan 23, 2024)
6-26385105-A-C		not specified	Uncertain significance (Feb 17, 2024)
6-26385126-G-A		not specified	Uncertain significance (Oct 05, 2022)
6-26385150-C-G		not specified	Uncertain significance (Nov 26, 2024)
6-26385152-G-A		not specified	Uncertain significance (Dec 15, 2022)
6-26385231-G-T		not specified	Uncertain significance (Sep 27, 2022)
6-26385274-C-T		BTN2A2-related disorder	Likely benign (Jul 12, 2019)
6-26385279-C-T		not specified	Uncertain significance (Jan 16, 2024)
6-26385302-C-T		not specified	Uncertain significance (Dec 28, 2022)
6-26385317-G-A		not specified	Uncertain significance (Nov 05, 2021)
6-26385330-A-T		not specified	Uncertain significance (Nov 26, 2024)
6-26385331-C-T		BTN2A2-related disorder	Likely benign (Apr 25, 2019)
6-26385347-C-T		not specified	Uncertain significance (Apr 25, 2023)
6-26385350-C-A		not specified	Uncertain significance (Jan 31, 2023)
6-26388005-C-G		BTN2A2-related disorder	Likely benign (Jul 29, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTN2A2	protein_coding	protein_coding	ENST00000356709	7	11779

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.38e-11	0.186	125600	1	147	125748	0.000589

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0390	295	293	1.01	0.0000163	3400
Missense in Polyphen		83	83.178	0.99786		1103
Synonymous	0.443	112	118	0.948	0.00000686	1058
Loss of Function	0.767	19	23.0	0.827	0.00000137	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00112
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00110	0.00109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000273	0.000273
Middle Eastern	0.00110	0.00109
South Asian	0.00196	0.00193
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits the proliferation of CD4 and CD8 T-cells activated by anti-CD3 antibodies, T-cell metabolism and IL2 and IFNG secretion. {ECO:0000250}.
• Pathway: Butyrophilin (BTN) family interactions;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.889
• rvis_EVS: 2.25
• rvis_percentile_EVS: 98.2

Haploinsufficiency Scores

• pHI: 0.0964
• hipred: N
• hipred_score: 0.132
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.271

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Btn2a2

Gene ontology

• Biological process: negative regulation of phosphatidylinositol 3-kinase signaling;negative regulation of cellular metabolic process;positive regulation of regulatory T cell differentiation;negative regulation of activated T cell proliferation;negative regulation of cytokine secretion;regulation of immune response;T cell receptor signaling pathway;negative regulation of T cell receptor signaling pathway;negative regulation of protein kinase B signaling;negative regulation of ERK1 and ERK2 cascade;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: plasma membrane;external side of plasma membrane;integral component of membrane
• Molecular function: signaling receptor binding;protein binding