BTLA

protein-coding

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

Gene summary

This gene encodes a member of the immunoglobulin superfamily. The encoded protein contains a single immunoglobulin (Ig) domain and is a receptor that relays inhibitory signals to suppress the immune response. Alternative splicing results in multiple transcript variants. Polymorphisms in this gene have been associated with an increased risk of rheumatoid arthritis. [provided by RefSeq, Aug 2011]

MANE transcript

NM_181780.4

Inheritance

—

ClinVar variants

U:20B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr3:112,461,067-112,499,472

External References & Databases

Ensembl (ENSG00000186265)

Transcript & Mutation Effects

hg38 • Region Span ~38.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BTLA variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 20

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181780.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			19 clinvar	1 clinvar		20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	20	1	0	21

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_181780.4	RefSeq	NP_861445.4	5	MANE Select
ENST00000334529.10	Ensembl	ENSP00000333919.5	5	MANE Select
NM_001085357.2	RefSeq	NP_001078826.1	4	Standard
ENST00000383680.4	Ensembl	ENSP00000373178.4	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vitamin D Receptor Pathway
Costimulation by the CD28 family
Immune System
Adaptive Immune System
BCR

Biological Process

adaptive immune response
immune response-regulating cell surface receptor signaling pathway
T cell costimulation

Molecular Function

signaling receptor activity

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334529
Coding exons: 5
Length: 35594
Individuals with no LoFs: 111368
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 111370
p: 0.00000898

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.46	96	146	0.659	0.00000647	1883
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00013	0.00013	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000096	0.0000096	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Lymphocyte inhibitory receptor which inhibits lymphocytes during immune response. {ECO:0000269|PubMed:12796776}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.534
RVIS EVS: 0.81
RVIS percentile EVS: 87.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.487

Gene Damage Prediction

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