TCAIM

T cell activation inhibitor, mitochondrial

Basic information

Region (hg38): 3:44338119-44409451

Previous symbols: [ "C3orf23" ]

Links

ENSG00000179152 ∙ NCBI:285343 ∙ ∙ HGNC:25241 ∙ Uniprot:Q8N3R3 ∙ 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 TCAIM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCAIM 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in TCAIM

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

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

Position	Type	Phenotype	Significance	ClinVar
3-44357757-A-G		not specified	Uncertain significance (Apr 23, 2024)
3-44357760-T-C		not specified	Uncertain significance (Apr 19, 2024)
3-44357794-C-T		not specified	Uncertain significance (Nov 06, 2023)
3-44357868-G-A		not specified	Likely benign (Nov 22, 2022)
3-44361462-A-T		not specified	Uncertain significance (Sep 01, 2021)
3-44361494-G-A		not specified	Uncertain significance (Jan 09, 2024)
3-44367561-A-G		not specified	Uncertain significance (Dec 27, 2023)
3-44367631-G-T		not specified	Uncertain significance (Oct 02, 2023)
3-44367687-C-T		not specified	Uncertain significance (Oct 12, 2021)
3-44392932-G-A		not specified	Uncertain significance (Jun 28, 2022)
3-44396425-C-T		not specified	Uncertain significance (May 30, 2023)
3-44396428-C-T		not specified	Uncertain significance (Dec 19, 2023)
3-44396492-C-T		not specified	Uncertain significance (Mar 20, 2023)
3-44396784-G-A		not specified	Uncertain significance (Feb 10, 2023)
3-44396787-G-A		not specified	Uncertain significance (Jan 09, 2023)
3-44400437-G-A		not specified	Uncertain significance (Feb 28, 2024)
3-44400448-G-A		not specified	Uncertain significance (Nov 14, 2023)
3-44400467-A-T		not specified	Uncertain significance (Jan 09, 2024)
3-44400507-T-A		not specified	Uncertain significance (Feb 26, 2024)
3-44400554-G-A		not specified	Likely benign (Jul 14, 2021)
3-44401256-T-C		not specified	Uncertain significance (Nov 02, 2023)
3-44401292-C-A		not specified	Uncertain significance (Nov 12, 2021)
3-44401333-G-A		not specified	Uncertain significance (Aug 10, 2021)
3-44407579-A-T		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCAIM	protein_coding	protein_coding	ENST00000342649	10	71333

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000223	0.996	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	198	257	0.772	0.0000125	3300
Missense in Polyphen		40	69.248	0.57763		847
Synonymous	1.01	76	88.1	0.863	0.00000424	875
Loss of Function	2.52	12	25.8	0.464	0.00000131	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000523	0.000461
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000381	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000381	0.000381
South Asian	0.000229	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate T-cell apoptosis. {ECO:0000250}.

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.0883
• hipred: N
• hipred_score: 0.397
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcaim
• Phenotype: skeleton phenotype

Gene ontology

• Cellular component: mitochondrion