TARM1

T cell-interacting, activating receptor on myeloid cells 1, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 19:54069895-54081365

Links

ENSG00000248385 ∙ NCBI:441864 ∙ OMIM:616802 ∙ HGNC:37250 ∙ Uniprot:B6A8C7 ∙ 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 TARM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TARM1 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in TARM1

This is a list of pathogenic ClinVar variants found in the TARM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54070059-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-54070110-G-C		not specified	Uncertain significance (Aug 11, 2022)
19-54070143-A-G		not specified	Uncertain significance (Jan 06, 2023)
19-54070149-T-C		not specified	Uncertain significance (Dec 05, 2022)
19-54070160-A-G		not specified	Uncertain significance (Nov 14, 2023)
19-54073959-C-T		not specified	Uncertain significance (Jan 24, 2023)
19-54073982-T-C		not specified	Uncertain significance (Sep 14, 2023)
19-54074003-C-G		not specified	Uncertain significance (Jun 24, 2022)
19-54074022-C-T		not specified	Uncertain significance (Jun 05, 2024)
19-54074054-G-A		not specified	Uncertain significance (Jun 27, 2022)
19-54074076-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-54074084-G-A		not specified	Uncertain significance (Oct 29, 2021)
19-54074132-C-T		not specified	Uncertain significance (May 26, 2023)
19-54074165-G-A		not specified	Uncertain significance (Aug 13, 2021)
19-54075033-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-54075042-C-T		not specified	Uncertain significance (Sep 17, 2021)
19-54075099-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-54075910-C-T		not specified	Likely benign (Apr 26, 2023)
19-54081313-A-G		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TARM1	protein_coding	protein_coding	ENST00000432826	5	11486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-7	0.205	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	114	152	0.750	0.00000821	1712
Missense in Polyphen		30	43.535	0.68909		549
Synonymous	1.27	52	65.0	0.800	0.00000397	578
Loss of Function	0.194	11	11.7	0.939	7.52e-7	117

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as receptor (By similarity). Negatively regulates TCR-mediated CD4(+) T cell proliferation and activation, possibly by binding an unknown ligand on the T cell surface (PubMed:26311901). Enhances Toll-like receptor-mediated production of pro-inflammatory cytokines by macrophages and neutrophils (By similarity). {ECO:0000250|UniProtKB:B6A8R8, ECO:0000269|PubMed:26311901}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Intolerance Scores

• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.48

Haploinsufficiency Scores

• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tarm1

Gene ontology

• Biological process: adaptive immune response;neutrophil degranulation;innate immune response;negative regulation of CD4-positive, alpha-beta T cell activation
• Cellular component: plasma membrane;integral component of membrane;specific granule membrane;tertiary granule membrane
• Molecular function: immunoglobulin receptor binding