BTLA

B and T lymphocyte associated, the group of CD molecules|Immunoglobulin like domain containing

Basic information

Region (hg38): 3:112463965-112499472

Links

ENSG00000186265 ∙ NCBI:151888 ∙ OMIM:607925 ∙ HGNC:21087 ∙ Uniprot:Q7Z6A9 ∙ 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 BTLA gene.

Variants pathogenicity by type

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

Variants in BTLA

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

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

Position	Type	Phenotype	Significance	ClinVar
3-112466176-T-A		not specified	Uncertain significance (Aug 21, 2023)
3-112466260-A-T		not specified	Uncertain significance (Dec 14, 2023)
3-112466292-T-A		not specified	Uncertain significance (Mar 07, 2024)
3-112469774-C-T		not specified	Uncertain significance (Dec 28, 2023)
3-112479634-T-A		not specified	Uncertain significance (Oct 06, 2021)
3-112479700-G-A		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTLA	protein_coding	protein_coding	ENST00000334529	5	35594

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0210	0.964	111368	0	2	111370	0.00000898

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	96	146	0.659	0.00000647	1883
Missense in Polyphen		18	37.747	0.47685		519
Synonymous	1.93	36	54.1	0.666	0.00000243	551
Loss of Function	2.12	5	13.4	0.374	6.61e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000127	0.000127
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000955	0.00000955
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lymphocyte inhibitory receptor which inhibits lymphocytes during immune response. {ECO:0000269|PubMed:12796776}.
• Pathway: Vitamin D Receptor Pathway;Costimulation by the CD28 family;Immune System;Adaptive Immune System;BCR (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.534
• rvis_EVS: 0.81
• rvis_percentile_EVS: 87.82

Haploinsufficiency Scores

• pHI: 0.0643
• hipred: Y
• hipred_score: 0.594
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.487

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Btla
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: adaptive immune response;immune response-regulating cell surface receptor signaling pathway;T cell costimulation
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: signaling receptor activity