BTNL3

butyrophilin like 3, the group of V-set domain containing|Butyrophilins

Basic information

Region (hg38): 5:180988846-181006727

Links

ENSG00000168903 ∙ NCBI:10917 ∙ OMIM:606192 ∙ HGNC:1143 ∙ Uniprot:Q6UXE8 ∙ 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 BTNL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTNL3 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			39	4	2	45
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	5	3

Variants in BTNL3

This is a list of pathogenic ClinVar variants found in the BTNL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-180989061-C-G			Benign (Jun 22, 2017)
5-180992816-A-G		not specified	Uncertain significance (Aug 11, 2024)
5-180992834-C-A		not specified	Uncertain significance (Nov 30, 2021)
5-180992872-G-A		not specified	Uncertain significance (Jul 20, 2021)
5-180992885-C-T		not specified	Uncertain significance (Jan 08, 2024)
5-180992900-C-T		not specified	Uncertain significance (Jan 31, 2025)
5-180992923-C-T		not specified	Uncertain significance (Feb 10, 2022)
5-180992924-G-A		not specified	Uncertain significance (Mar 17, 2023)
5-180992924-G-C		not specified	Uncertain significance (Nov 13, 2024)
5-180992980-T-C		not specified	Uncertain significance (Apr 15, 2024)
5-180993097-T-C		not specified	Uncertain significance (Nov 10, 2022)
5-180993134-A-C		not specified	Uncertain significance (Dec 19, 2023)
5-180993151-C-T			Benign/Likely benign (Apr 01, 2023)
5-180993152-G-A		not specified	Likely benign (Dec 15, 2022)
5-180993154-G-T		not specified	Uncertain significance (Jan 16, 2025)
5-180997241-C-T			Benign (Jun 22, 2017)
5-180997348-A-G		not specified	Uncertain significance (Jan 21, 2025)
5-180997381-A-G		not specified	Uncertain significance (Nov 26, 2024)
5-180997402-T-C		not specified	Uncertain significance (Aug 26, 2024)
5-180997423-G-C			Benign (Apr 19, 2018)
5-180997431-T-C		not specified	Uncertain significance (Mar 08, 2024)
5-181002692-C-G		not specified	Uncertain significance (Dec 07, 2024)
5-181002698-C-T		not specified	Uncertain significance (Nov 09, 2024)
5-181002710-A-G		not specified	Uncertain significance (Jan 30, 2024)
5-181002754-G-A		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTNL3	protein_coding	protein_coding	ENST00000342868	8	17883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000597	0.978	125147	3	13	125163	0.0000639

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.677	229	260	0.882	0.0000140	3011
Missense in Polyphen		56	68.608	0.81624		915
Synonymous	0.867	92	103	0.891	0.00000599	911
Loss of Function	2.03	8	17.0	0.470	7.88e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000444	0.000353
Ashkenazi Jewish	0.00	0.00
East Asian	0.000233	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000510	0.0000265
Middle Eastern	0.000233	0.000217
South Asian	0.0000681	0.0000653
Other	0.000190	0.000164

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0614

Intolerance Scores

• loftool: 0.784
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.8

Haploinsufficiency Scores

• pHI: 0.0347
• hipred: N
• hipred_score: 0.301

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

Gene Damage Prediction

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

Gene ontology

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