BTN2A1

butyrophilin subfamily 2 member A1, the group of V-set domain containing|C2-set domain containing|Butyrophilins

Basic information

Region (hg38): 6:26457903-26476621

Links

ENSG00000112763 ∙ NCBI:11120 ∙ OMIM:613590 ∙ HGNC:1136 ∙ Uniprot:Q7KYR7 ∙ 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 BTN2A1 gene.

• Inborn genetic diseases (31 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTN2A1 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			26	5		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	5	1

Variants in BTN2A1

This is a list of pathogenic ClinVar variants found in the BTN2A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-26458660-C-A		not specified	Uncertain significance (May 27, 2022)
6-26458667-C-T		not specified	Uncertain significance (Jun 09, 2022)
6-26459579-G-A		not specified	Uncertain significance (Sep 14, 2023)
6-26459592-G-A		not specified	Uncertain significance (Sep 16, 2021)
6-26459636-G-T		not specified	Uncertain significance (Aug 30, 2021)
6-26459671-G-C		not specified	Uncertain significance (Jan 09, 2024)
6-26459718-G-T		not specified	Uncertain significance (Aug 16, 2022)
6-26459733-T-C		not specified	Uncertain significance (Feb 11, 2022)
6-26459787-G-A		not specified	Uncertain significance (Jan 06, 2023)
6-26459798-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-26459807-A-G		not specified	Uncertain significance (Sep 20, 2023)
6-26463279-C-T		not specified	Uncertain significance (Sep 17, 2021)
6-26463323-G-T		not specified	Uncertain significance (Jul 20, 2022)
6-26463360-G-A		not specified	Likely benign (Jan 03, 2024)
6-26463370-C-T		not specified	Likely benign (Dec 07, 2021)
6-26463394-T-C		not specified	Likely benign (May 23, 2023)
6-26463408-G-A		not specified	Uncertain significance (Jun 11, 2021)
6-26463464-G-A		not specified	Uncertain significance (Apr 25, 2022)
6-26463492-G-A		not specified	Likely benign (Jun 29, 2023)
6-26463501-A-G		not specified	Uncertain significance (May 03, 2023)
6-26465220-G-A		not specified	Uncertain significance (Dec 04, 2023)
6-26465262-G-A		not specified	Likely benign (Aug 10, 2021)
6-26465290-A-C		not specified	Uncertain significance (Dec 20, 2022)
6-26465302-A-G		not specified	Uncertain significance (Feb 22, 2023)
6-26465331-C-T		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTN2A1	protein_coding	protein_coding	ENST00000312541	7	18700

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.40e-21	0.0000834	125575	0	173	125748	0.000688

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.438	321	300	1.07	0.0000177	3424
Missense in Polyphen		95	80.649	1.178		1054
Synonymous	-1.27	141	123	1.15	0.00000766	1068
Loss of Function	-1.53	27	19.7	1.37	0.00000111	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00130	0.00131
Finnish	0.00	0.00
European (Non-Finnish)	0.000819	0.000818
Middle Eastern	0.00130	0.00131
South Asian	0.000523	0.000523
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0898

Intolerance Scores

• loftool: 0.979
• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.87

Haploinsufficiency Scores

• pHI: 0.0694
• hipred: N
• hipred_score: 0.148
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.242

Gene Damage Prediction

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

Gene ontology

• Biological process: lipid metabolic process;regulation of immune response;T cell receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane
• Molecular function: molecular_function;signaling receptor binding