BTN3A3

butyrophilin subfamily 3 member A3, the group of V-set domain containing|Butyrophilins

Basic information

Region (hg38): 6:26440471-26453415

Links

ENSG00000111801 ∙ NCBI:10384 ∙ OMIM:613595 ∙ HGNC:1140 ∙ Uniprot:O00478 ∙ 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 BTN3A3 gene.

• Inborn genetic diseases (30 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTN3A3 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				2		2
missense			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	4	0

Variants in BTN3A3

This is a list of pathogenic ClinVar variants found in the BTN3A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-26443588-G-A		not specified	Uncertain significance (Mar 24, 2023)
6-26443618-A-G		not specified	Uncertain significance (Mar 12, 2024)
6-26444038-C-T		not specified	Uncertain significance (Dec 15, 2023)
6-26444074-T-G		not specified	Uncertain significance (Aug 16, 2022)
6-26444075-G-A			Likely benign (Mar 01, 2023)
6-26444110-C-T		not specified	Uncertain significance (Feb 27, 2023)
6-26444172-C-T		not specified	Uncertain significance (Aug 09, 2021)
6-26444196-G-C		not specified	Uncertain significance (Jul 06, 2021)
6-26444202-C-T		not specified	Uncertain significance (Apr 18, 2023)
6-26444224-C-T		not specified	Uncertain significance (May 27, 2022)
6-26445793-C-T		not specified	Uncertain significance (Feb 17, 2024)
6-26445798-A-C		not specified	Uncertain significance (Jul 13, 2022)
6-26445811-G-A		not specified	Likely benign (Aug 02, 2023)
6-26445847-C-A		not specified	Uncertain significance (Oct 05, 2021)
6-26445944-C-T		not specified	Uncertain significance (Aug 28, 2023)
6-26445949-C-A		not specified	Uncertain significance (Jan 16, 2024)
6-26445979-A-G		not specified	Uncertain significance (Jun 18, 2021)
6-26448250-C-G		not specified	Uncertain significance (Jul 15, 2021)
6-26448281-C-T		not specified	Uncertain significance (Apr 25, 2023)
6-26449667-G-A		not specified	Uncertain significance (Aug 09, 2021)
6-26451734-A-G		not specified	Uncertain significance (Oct 27, 2021)
6-26451761-C-T		not specified	Uncertain significance (Dec 28, 2022)
6-26451773-G-C		not specified	Uncertain significance (Mar 22, 2022)
6-26451798-G-A		not specified	Uncertain significance (Oct 05, 2023)
6-26451865-C-A		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTN3A3	protein_coding	protein_coding	ENST00000244519	9	12944

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-18	0.000710	123785	33	1929	125747	0.00783

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.152	335	327	1.02	0.0000179	3789
Missense in Polyphen		91	84.579	1.0759		1074
Synonymous	-1.00	145	130	1.11	0.00000798	1183
Loss of Function	-0.850	25	20.8	1.20	0.00000122	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00755	0.00749
Ashkenazi Jewish	0.0449	0.0444
East Asian	0.00228	0.00223
Finnish	0.00448	0.00444
European (Non-Finnish)	0.00750	0.00742
Middle Eastern	0.00228	0.00223
South Asian	0.00859	0.00850
Other	0.0117	0.0116

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in T-cell responses in the adaptive immune response. {ECO:0000269|PubMed:22767497}.
• Pathway: Butyrophilin (BTN) family interactions;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0958

Intolerance Scores

• loftool: 0.988
• rvis_EVS: -0.28
• rvis_percentile_EVS: 33.49

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.112
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.447

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Btf3
• Phenotype: reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

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