BTN2A2
Basic information
Region (hg38): 6:26383096-26394874
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTN2A2 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 | 7 | |||||
missense | 33 | 48 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 2 | 2 | ||||
non coding | 1 | |||||
Total | 0 | 0 | 33 | 11 | 12 |
Variants in BTN2A2
This is a list of pathogenic ClinVar variants found in the BTN2A2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-26383832-C-T | Benign (Jan 03, 2019) | |||
6-26383834-G-A | not specified | Uncertain significance (Feb 27, 2023) | ||
6-26383864-C-T | not specified | Uncertain significance (Mar 20, 2023) | ||
6-26383868-T-C | not specified | Uncertain significance (Oct 18, 2021) | ||
6-26383878-G-A | BTN2A2-related disorder | Benign (Apr 29, 2019) | ||
6-26385032-G-T | not specified | Uncertain significance (Oct 03, 2023) | ||
6-26385035-C-A | not specified | Uncertain significance (Oct 17, 2023) | ||
6-26385035-C-G | Benign (Jan 03, 2019) | |||
6-26385063-G-T | not specified | Uncertain significance (May 27, 2022) | ||
6-26385098-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
6-26385105-A-C | not specified | Uncertain significance (Feb 17, 2024) | ||
6-26385126-G-A | not specified | Uncertain significance (Oct 05, 2022) | ||
6-26385152-G-A | not specified | Uncertain significance (Dec 15, 2022) | ||
6-26385231-G-T | not specified | Uncertain significance (Sep 27, 2022) | ||
6-26385274-C-T | BTN2A2-related disorder | Likely benign (Jul 12, 2019) | ||
6-26385279-C-T | not specified | Uncertain significance (Jan 16, 2024) | ||
6-26385302-C-T | not specified | Uncertain significance (Dec 28, 2022) | ||
6-26385317-G-A | not specified | Uncertain significance (Nov 05, 2021) | ||
6-26385331-C-T | BTN2A2-related disorder | Likely benign (Apr 25, 2019) | ||
6-26385347-C-T | not specified | Uncertain significance (Apr 25, 2023) | ||
6-26385350-C-A | not specified | Uncertain significance (Jan 31, 2023) | ||
6-26388005-C-G | BTN2A2-related disorder | Likely benign (Jul 29, 2019) | ||
6-26388129-G-A | not specified | Likely benign (Sep 29, 2023) | ||
6-26388144-G-T | BTN2A2-related disorder | Likely benign (Feb 01, 2022) | ||
6-26388177-G-A | BTN2A2-related disorder | Benign (Nov 06, 2019) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
BTN2A2 | protein_coding | protein_coding | ENST00000356709 | 7 | 11779 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.38e-11 | 0.186 | 125600 | 1 | 147 | 125748 | 0.000589 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.0390 | 295 | 293 | 1.01 | 0.0000163 | 3400 |
Missense in Polyphen | 83 | 83.178 | 0.99786 | 1103 | ||
Synonymous | 0.443 | 112 | 118 | 0.948 | 0.00000686 | 1058 |
Loss of Function | 0.767 | 19 | 23.0 | 0.827 | 0.00000137 | 234 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00112 | 0.00112 |
Ashkenazi Jewish | 0.000298 | 0.000298 |
East Asian | 0.00110 | 0.00109 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000273 | 0.000273 |
Middle Eastern | 0.00110 | 0.00109 |
South Asian | 0.00196 | 0.00193 |
Other | 0.000328 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibits the proliferation of CD4 and CD8 T-cells activated by anti-CD3 antibodies, T-cell metabolism and IL2 and IFNG secretion. {ECO:0000250}.;
- Pathway
- Butyrophilin (BTN) family interactions;Immune System;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.125
Intolerance Scores
- loftool
- 0.889
- rvis_EVS
- 2.25
- rvis_percentile_EVS
- 98.2
Haploinsufficiency Scores
- pHI
- 0.0964
- hipred
- N
- hipred_score
- 0.132
- ghis
- 0.408
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.271
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Btn2a2
- Phenotype
Gene ontology
- Biological process
- negative regulation of phosphatidylinositol 3-kinase signaling;negative regulation of cellular metabolic process;positive regulation of regulatory T cell differentiation;negative regulation of activated T cell proliferation;negative regulation of cytokine secretion;regulation of immune response;T cell receptor signaling pathway;negative regulation of T cell receptor signaling pathway;negative regulation of protein kinase B signaling;negative regulation of ERK1 and ERK2 cascade;negative regulation of G1/S transition of mitotic cell cycle
- Cellular component
- plasma membrane;external side of plasma membrane;integral component of membrane
- Molecular function
- signaling receptor binding;protein binding