BTNL9

butyrophilin like 9, the group of V-set domain containing|Butyrophilins

Basic information

Region (hg38): 5:181040224-181061521

Links

ENSG00000165810 ∙ NCBI:153579 ∙ ∙ HGNC:24176 ∙ Uniprot:Q6UXG8 ∙ 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 BTNL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTNL9 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					4	4
missense			49	1		50
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	49	1	6

Variants in BTNL9

This is a list of pathogenic ClinVar variants found in the BTNL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-181045563-A-G		not specified	Uncertain significance (May 10, 2024)
5-181045589-C-T		not specified	Uncertain significance (May 04, 2022)
5-181045592-A-G		not specified	Uncertain significance (Jun 11, 2021)
5-181047990-C-T		not specified	Uncertain significance (Apr 11, 2023)
5-181048034-C-T		not specified	Uncertain significance (May 20, 2024)
5-181048100-A-G		not specified	Uncertain significance (Aug 15, 2023)
5-181048110-C-G		not specified	Uncertain significance (Jan 09, 2024)
5-181048110-C-T		not specified	Uncertain significance (Dec 20, 2021)
5-181048112-G-C		not specified	Uncertain significance (Jan 04, 2024)
5-181048113-C-T		not specified	Uncertain significance (Jun 02, 2024)
5-181048118-C-T		not specified	Uncertain significance (Dec 04, 2023)
5-181048145-G-A		not specified	Uncertain significance (May 05, 2023)
5-181048163-G-A		not specified	Uncertain significance (Sep 16, 2021)
5-181048195-T-C			Benign (Apr 05, 2018)
5-181048202-G-A		not specified	Uncertain significance (May 26, 2023)
5-181048218-G-A		not specified	Uncertain significance (Mar 21, 2022)
5-181048229-G-A		not specified	Uncertain significance (May 23, 2023)
5-181048242-G-C		not specified	Uncertain significance (Jan 23, 2023)
5-181048247-G-C		not specified	Uncertain significance (Jan 16, 2024)
5-181050232-C-T		not specified	Uncertain significance (Jan 02, 2024)
5-181050237-G-A		not specified	Likely benign (Aug 23, 2021)
5-181050253-AC-A			Benign (Jan 01, 2023)
5-181050312-G-A		not specified	Uncertain significance (Sep 16, 2021)
5-181050364-T-C		not specified	Uncertain significance (Jun 09, 2022)
5-181053214-G-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTNL9	protein_coding	protein_coding	ENST00000327705	10	21299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.88e-14	0.0352	123855	9	1884	125748	0.00756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.554	319	292	1.09	0.0000151	3380
Missense in Polyphen		117	98.985	1.182		1216
Synonymous	-0.556	145	137	1.06	0.00000753	1104
Loss of Function	0.277	21	22.4	0.937	0.00000105	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0112	0.0112
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.00261	0.00261
Finnish	0.000742	0.000739
European (Non-Finnish)	0.0101	0.0101
Middle Eastern	0.00261	0.00261
South Asian	0.00938	0.00925
Other	0.00782	0.00785

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.882
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.180
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0803

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Btnl9

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