BTNL2

butyrophilin like 2, the group of V-set domain containing|C2-set domain containing|Butyrophilins

Basic information

Region (hg38): 6:32393338-32407181

Links

ENSG00000204290 ∙ NCBI:56244 ∙ OMIM:606000 ∙ HGNC:1142 ∙ Uniprot:Q9UIR0 ∙ 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 BTNL2 gene.

• Inborn genetic diseases (12 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTNL2 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			11	1	2	14
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1			1
Total	0	0	12	1	4

Variants in BTNL2

This is a list of pathogenic ClinVar variants found in the BTNL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-32394744-C-G		not specified	Uncertain significance (Nov 29, 2023)
6-32394774-C-T		not specified	Uncertain significance (Jul 07, 2022)
6-32394816-C-T		not specified	Uncertain significance (Apr 28, 2022)
6-32394902-G-A			Benign (Mar 30, 2018)
6-32394953-T-C		not specified	Uncertain significance (Oct 26, 2022)
6-32396039-T-T		Sarcoidosis, susceptibility to, 2	risk factor (Apr 01, 2005)
6-32396068-T-G		not specified	Uncertain significance (Dec 08, 2023)
6-32396099-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-32396120-G-T		not specified	Likely benign (May 28, 2023)
6-32396201-C-T		not specified	Uncertain significance (May 27, 2022)
6-32396360-G-C		not specified	Uncertain significance (Jul 14, 2022)
6-32402929-A-G			Uncertain significance (May 26, 2023)
6-32402952-G-A		not specified	Uncertain significance (Aug 08, 2023)
6-32403082-C-T			Benign (May 29, 2018)
6-32403129-T-C		not specified	Uncertain significance (Jan 10, 2023)
6-32403192-TG-T			Benign (Jul 15, 2020)
6-32405004-T-C		not specified	Uncertain significance (Aug 12, 2021)
6-32405020-G-A		not specified	Uncertain significance (Feb 05, 2024)
6-32405151-G-T		not specified	Uncertain significance (Dec 27, 2023)
6-32405166-C-T		not specified	Uncertain significance (Jun 22, 2023)
6-32405265-G-C		not specified	Uncertain significance (Mar 01, 2023)
6-32405570-G-C			Uncertain significance (Jun 11, 2021)
6-32407084-C-A		not specified	Uncertain significance (Mar 16, 2022)
6-32407086-A-C		not specified	Uncertain significance (Mar 07, 2024)
6-32407088-T-C			Benign (Oct 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTNL2	protein_coding	protein_coding	ENST00000454136	7	13166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.56e-11	0.150	100966	1860	22922	125748	0.104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	194	263	0.739	0.0000135	3104
Missense in Polyphen		59	85.132	0.69304		1087
Synonymous	0.885	98	110	0.893	0.00000648	950
Loss of Function	0.546	17	19.6	0.867	8.40e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.356	0.341
Ashkenazi Jewish	0.0334	0.0327
East Asian	0.194	0.186
Finnish	0.165	0.157
European (Non-Finnish)	0.0707	0.0663
Middle Eastern	0.194	0.186
South Asian	0.0853	0.0814
Other	0.101	0.0967

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of T-cell proliferation. {ECO:0000250}.
• Disease: DISEASE: Sarcoidosis 2 (SS2) [MIM:612387]: An idiopathic, systemic, inflammatory disease characterized by the formation of immune granulomas in involved organs. Granulomas predominantly invade the lungs and the lymphatic system, but also skin, liver, spleen, eyes and other organs may be involved. {ECO:0000269|PubMed:15735647}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. A nucleotide transition affecting a splice donor site results in the use of an alternative splice site and the production of isoform 3. Individuals expressing isoform 3 have a higher risk for sarcoidosis.
• Pathway: Butyrophilin (BTN) family interactions;Immune System;Adaptive Immune System (Consensus)

Haploinsufficiency Scores

• pHI: 0.0567
• hipred: N
• hipred_score: 0.153
• ghis: 0.394

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0448

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Btnl2

Gene ontology

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