BTN1A1

butyrophilin subfamily 1 member A1, the group of V-set domain containing|C2-set domain containing|Butyrophilins

Basic information

Region (hg38): 6:26500303-26510425

Previous symbols: [ "BTN" ]

Links

ENSG00000124557 ∙ NCBI:696 ∙ OMIM:601610 ∙ HGNC:1135 ∙ Uniprot:Q13410 ∙ 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 BTN1A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTN1A1 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						0
missense			32	1	2	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	32	1	2

Variants in BTN1A1

This is a list of pathogenic ClinVar variants found in the BTN1A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-26501299-C-T		not specified	Uncertain significance (Oct 30, 2023)
6-26501302-A-G		not specified	Uncertain significance (Jun 16, 2024)
6-26501318-G-C		not specified	Uncertain significance (Feb 04, 2025)
6-26501336-T-C		not specified	Uncertain significance (Sep 01, 2021)
6-26501671-C-G		not specified	Uncertain significance (Sep 03, 2024)
6-26501679-A-T		not specified	Uncertain significance (Aug 02, 2023)
6-26501683-C-G		not specified	Uncertain significance (Jan 08, 2025)
6-26501692-T-C		not specified	Uncertain significance (Jun 18, 2021)
6-26501715-A-G		not specified	Uncertain significance (Sep 09, 2021)
6-26501737-T-G		not specified	Uncertain significance (Feb 18, 2025)
6-26501749-G-C		not specified	Uncertain significance (Jun 16, 2023)
6-26501824-G-C		not specified	Uncertain significance (Sep 20, 2024)
6-26501930-G-T		not specified	Uncertain significance (Aug 30, 2021)
6-26504994-C-T		not specified	Uncertain significance (May 13, 2022)
6-26505002-T-A		not specified	Uncertain significance (Jan 24, 2025)
6-26505009-C-G		not specified	Uncertain significance (Mar 14, 2023)
6-26505041-G-A		not specified	Uncertain significance (Nov 08, 2024)
6-26505042-G-C		not specified	Uncertain significance (May 09, 2022)
6-26505123-G-T		not specified	Uncertain significance (Dec 12, 2023)
6-26505135-C-T		not specified	Likely benign (Jun 16, 2024)
6-26505201-T-C		not specified	Uncertain significance (Aug 28, 2024)
6-26506707-C-T		not specified	Uncertain significance (Oct 21, 2024)
6-26506709-T-A		not specified	Uncertain significance (Jun 07, 2024)
6-26506737-T-C		not specified	Uncertain significance (Aug 13, 2021)
6-26506758-T-C		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTN1A1	protein_coding	protein_coding	ENST00000244513	7	9202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.95e-8	0.670	125670	0	78	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	229	293	0.783	0.0000144	3383
Missense in Polyphen		64	101.67	0.62946		1216
Synonymous	1.67	95	118	0.805	0.00000577	1090
Loss of Function	1.26	15	21.3	0.704	9.81e-7	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00204	0.00192
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000240	0.000237
Middle Eastern	0.0000544	0.0000544
South Asian	0.000328	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in the secretion of milk-fat droplets. May act as a specific membrane-associated receptor for the association of cytoplasmic droplets with the apical plasma membrane (By similarity). Inhibits the proliferation of CD4 and CD8 T-cells activated by anti-CD3 antibodies, T-cell metabolism and IL2 and IFNG secretion (By similarity). {ECO:0000250}.
• Pathway: Butyrophilin (BTN) family interactions;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.882
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.36

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00414

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Btn1a1
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

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